Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,975,051 G→A A38V (GCC→GTC)  motA ← MotA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,975,0510GA99.2% 466.4 / ‑5.3 132A38V (GCC→GTC) motAMotA
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (71/60);  total (71/61)
Fisher's exact test for biased strand distribution p-value = 4.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

Only 100 of 136 total aligned reads displayed.

GAGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGGCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACC  >  NC_000913/1974961‑1975140
                                                                                          |                                                                                         
 aGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACaa                                                                                        <  2:1648200/93‑1 (MQ=255)
     acgaAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACaataat                                                                                    <  2:3196828/93‑1 (MQ=255)
     acgaAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACaataat                                                                                    >  1:3967350/1‑93 (MQ=255)
      cgaAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATc                                                                                   >  2:3993522/1‑93 (MQ=255)
        aaaCAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCAc                                                                                 >  1:2614719/1‑93 (MQ=255)
         aaCAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCAcc                                                                                <  2:2608867/93‑1 (MQ=255)
          aCAGCAACGGCAGCGCCTTCAGCTTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCa                                                                               <  2:4177745/93‑1 (MQ=255)
          aCAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCa                                                                               <  2:638088/93‑1 (MQ=255)
          aCAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCa                                                                               <  2:4677050/93‑1 (MQ=255)
           cAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAg                                                                              <  2:3252548/93‑1 (MQ=255)
            aGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGt                                                                             <  1:3292878/93‑1 (MQ=255)
            aGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGt                                                                             >  2:1511917/1‑93 (MQ=255)
             gCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGtt                                                                            <  2:4184996/93‑1 (MQ=255)
             gCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGtt                                                                            >  1:2226409/1‑93 (MQ=255)
             gCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGtt                                                                            >  2:1096758/1‑93 (MQ=255)
              cAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTc                                                                           <  2:1014544/93‑1 (MQ=255)
              cAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTc                                                                           >  2:4553214/1‑93 (MQ=255)
               aaCGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCCGTTCa                                                                          >  1:3674328/1‑93 (MQ=255)
               aaCGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCa                                                                          <  2:3005389/93‑1 (MQ=255)
                aCGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAg                                                                         <  1:2348314/93‑1 (MQ=255)
                   gCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCgg                                                                      >  2:659614/1‑93 (MQ=255)
                    cAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCggg                                                                     >  1:923419/1‑93 (MQ=255)
                     aGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGt                                                                    <  1:677731/93‑1 (MQ=255)
                     aGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGt                                                                    <  1:404889/93‑1 (MQ=255)
                     aGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGt                                                                    <  1:1793091/93‑1 (MQ=255)
                      gcgcCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGtt                                                                   >  2:3572493/1‑93 (MQ=255)
                       cgcCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCGAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGttt                                                                  >  1:3488452/1‑92 (MQ=255)
                        gcCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGa                                                                 >  2:2582102/1‑93 (MQ=255)
                        gcCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGa                                                                 >  1:4667030/1‑93 (MQ=255)
                         ccTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGAt                                                                >  1:4291032/1‑93 (MQ=255)
                         ccTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGAACCAATCCCTGCACCGACAATAATCACTAGTTCAGCGTGCTGAt                                                                >  2:507236/1‑93 (MQ=255)
                          cTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATa                                                               >  1:3256905/1‑93 (MQ=255)
                          cTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATa                                                               <  2:3776421/93‑1 (MQ=255)
                           ttCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATag                                                              <  1:3350613/93‑1 (MQ=255)
                           gtCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATag                                                              <  1:1516614/92‑1 (MQ=255)
                            tCAGCGTGCCTTTAATCGCTTTTCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATaga                                                             <  1:2735093/93‑1 (MQ=255)
                            tCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATaga                                                             <  1:182540/93‑1 (MQ=255)
                            tCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATaga                                                             <  1:1416435/93‑1 (MQ=255)
                             cAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATagag                                                            <  1:855595/93‑1 (MQ=255)
                                cGTGTCTTTAATCGCTTTGCCATTATTCCCGACGATAACCGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGc                                                         <  2:883634/93‑1 (MQ=255)
                                  tGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTc                                                       >  2:2406728/1‑93 (MQ=255)
                                   gCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTcc                                                      >  2:3965527/1‑93 (MQ=255)
                                   gCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTcc                                                      >  1:3071298/1‑93 (MQ=255)
                                    ccTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCa                                                     >  1:3574539/1‑93 (MQ=255)
                                     cTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCGCCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCaa                                                    >  2:4619034/1‑93 (MQ=255)
                                     cTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCaa                                                    <  2:4249227/93‑1 (MQ=255)
                                      tttAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAg                                                   >  2:1661304/1‑93 (MQ=255)
                                       ttAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAgg                                                  >  2:2749138/1‑93 (MQ=255)
                                            cGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTcc                                             <  1:73576/93‑1 (MQ=255)
                                              cTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCAc                                           <  1:1768205/93‑1 (MQ=255)
                                              cTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCAc                                           <  2:1479979/93‑1 (MQ=255)
                                              cTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCAc                                           >  2:2541757/1‑93 (MQ=255)
                                                 tGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCgg                                        >  2:1943183/1‑93 (MQ=255)
                                                   ccATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGtc                                      <  2:2611345/93‑1 (MQ=255)
                                                    cATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGtca                                     >  1:1129441/1‑93 (MQ=255)
                                                    cATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGtca                                     <  1:2130663/93‑1 (MQ=255)
                                                     attattGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGtcat                                    >  2:289947/1‑93 (MQ=255)
                                                      ttattGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGtcatc                                   <  2:4308065/93‑1 (MQ=255)
                                                      ttattGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGtcatc                                   >  2:2182813/1‑93 (MQ=255)
                                                         ttGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCaaa                                >  2:813723/1‑93 (MQ=255)
                                                           gCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATa                              >  2:2552301/1‑93 (MQ=255)
                                                           gCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATa                              <  2:1625634/93‑1 (MQ=255)
                                                           gCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATa                              <  2:1577823/93‑1 (MQ=255)
                                                             cgacgaTAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAAc                            <  2:1098211/93‑1 (MQ=255)
                                                              gacgaTAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGGTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAAcc                           >  2:4610587/1‑93 (MQ=255)
                                                              cacgaTAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAAcc                           <  2:2130166/92‑1 (MQ=255)
                                                                cgaTAAACGACCCAATCCCTGCACCGACAATAATCGCCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAAccgc                         <  1:3876178/93‑1 (MQ=255)
                                                                cgaTAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGCTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAAccgc                         >  2:1325355/1‑93 (MQ=255)
                                                                 gaTAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAAccgcc                        >  1:2722284/1‑93 (MQ=255)
                                                                   tAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGa                      >  2:4251086/1‑93 (MQ=255)
                                                                   tAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGa                      >  2:1451322/1‑93 (MQ=255)
                                                                   tAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGa                      >  1:2976921/1‑93 (MQ=255)
                                                                      aCGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGaaaa                   >  2:2404806/1‑93 (MQ=255)
                                                                      aCGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGaaaa                   >  2:1459684/1‑93 (MQ=255)
                                                                      aCGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGaaaa                   <  2:3290372/93‑1 (MQ=255)
                                                                       cGACCCAATCCCTGCACCTACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAAc                  <  1:1418391/93‑1 (MQ=255)
                                                                       cGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAAc                  <  2:2231271/93‑1 (MQ=255)
                                                                       cGACACAATCCCTGCACCGGCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAAc                  <  1:929055/93‑1 (MQ=255)
                                                                        gACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACt                 <  1:1215735/93‑1 (MQ=255)
                                                                        gACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACt                 >  2:1372069/1‑93 (MQ=255)
                                                                          cccAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGt               >  1:1401630/1‑93 (MQ=255)
                                                                           ccAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTa              <  1:4487365/93‑1 (MQ=255)
                                                                            cAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTAc             <  1:3814426/93‑1 (MQ=255)
                                                                             caccccTGCACCGCCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTAcc            <  1:1137634/90‑1 (MQ=255)
                                                                             aaTCCCTGCACCAACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTAcc            >  1:2532300/1‑93 (MQ=255)
                                                                              aTCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCg           >  1:663604/1‑93 (MQ=255)
                                                                               tCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCga          <  1:421734/93‑1 (MQ=255)
                                                                               tCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCga          >  1:4102873/1‑93 (MQ=255)
                                                                               tCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCga          <  1:1638627/93‑1 (MQ=255)
                                                                               tCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCga          >  2:2270704/1‑93 (MQ=255)
                                                                                cccTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCgag         >  2:2416338/1‑93 (MQ=255)
                                                                                 ccTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCgaga        <  2:4370833/93‑1 (MQ=255)
                                                                                  cTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGaa       <  1:2450175/93‑1 (MQ=255)
                                                                                  cTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGaa       >  1:2449209/1‑93 (MQ=255)
                                                                                   tGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGaac      >  1:3991413/1‑93 (MQ=255)
                                                                                   tGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGaac      <  2:3415896/93‑1 (MQ=255)
                                                                                     cACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGaacaa    <  2:4061055/93‑1 (MQ=255)
                                                                                      aCCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGaacaac   >  2:4095323/1‑93 (MQ=255)
                                                                                       ccGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAAcc  >  1:330160/1‑93 (MQ=255)
                                                                                       ccGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAAcc  <  2:1535899/93‑1 (MQ=255)
                                                                                          |                                                                                         
GAGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGGCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACC  >  NC_000913/1974961‑1975140

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGGAGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGGCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAGGT  >  NC_000913/1974959‑1975144
                                                                                            |                                                                                             
TGGAGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGAC                                                                                              <  SRR4302535.3969019/94‑1 (MQ=60)
 GGAGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACA                                                                                             <  SRR4302535.1585157/94‑1 (MQ=60)
   AGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAAT                                                                                           <  SRR4302535.2417805/94‑1 (MQ=60)
      GACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAAT                                                                                        >  SRR4302535.3994450/1‑94 (MQ=60)
      GACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAAT                                                                                        >  SRR4302535.1803100/1‑94 (MQ=60)
         GAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCAC                                                                                     >  SRR4302535.2633469/1‑94 (MQ=60)
              AGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTT                                                                                <  SRR4302535.3315773/94‑1 (MQ=60)
              AGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTT                                                                                >  SRR4302535.2242250/1‑94 (MQ=60)
                CAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCCGTTCA                                                                              >  SRR4302535.3699770/1‑94 (MQ=60)
                CAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCA                                                                              >  SRR4302535.2198601/1‑94 (MQ=60)
                  ACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGC                                                                            <  SRR4302535.2365150/94‑1 (MQ=60)
                   CGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCG                                                                           <  SRR4302535.3367165/94‑1 (MQ=60)
                     GCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGG                                                                         >  SRR4302535.929961/1‑94 (MQ=60)
                       AGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTT                                                                       >  SRR4302535.3287283/1‑94 (MQ=60)
                       AGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTT                                                                       <  SRR4302535.682467/94‑1 (MQ=60)
                       AGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTT                                                                       <  SRR4302535.407724/94‑1 (MQ=60)
                       AGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTT                                                                       <  SRR4302535.1806055/94‑1 (MQ=60)
                       AGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTT                                                                       <  SRR4302535.4091628/94‑1 (MQ=60)
                        GCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCGAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTT                                                                      >  SRR4302535.3512671/1‑94 (MQ=60)
                         CGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGA                                                                     >  SRR4302535.4698573/1‑94 (MQ=60)
                          GCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGAT                                                                    >  SRR4302535.4320399/1‑94 (MQ=60)
                           CCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATA                                                                   >  SRR4302535.3279534/1‑94 (MQ=60)
                             TTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGA                                                                 <  SRR4302535.3373954/94‑1 (MQ=60)
                             GTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGA                                                                 <  SRR4302535.1527539/94‑1 (MQ=60)
                              TCAGCGTGCCTTTAATCGCTTTTCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAG                                                                <  SRR4302535.2754607/94‑1 (MQ=60)
                              TCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAG                                                                <  SRR4302535.183800/94‑1 (MQ=60)
                              TCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAG                                                                <  SRR4302535.1426547/94‑1 (MQ=60)
                               CAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGT                                                               <  SRR4302535.861628/94‑1 (MQ=60)
                                  CGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCT                                                            >  SRR4302535.939516/1‑94 (MQ=60)
                                    TGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCC                                                          >  SRR4302535.3092744/1‑94 (MQ=60)
                                     GCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCA                                                         >  SRR4302535.3599321/1‑94 (MQ=60)
                                     GCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCA                                                         <  SRR4302535.4472425/94‑1 (MQ=60)
                                     GCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCA                                                         <  SRR4302535.484209/94‑1 (MQ=60)
                                              CGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCA                                                >  SRR4302535.1364912/1‑94 (MQ=60)
                                              CGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCA                                                <  SRR4302535.74109/94‑1 (MQ=60)
                                                CTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACC                                              >  SRR4302535.2584259/1‑94 (MQ=60)
                                                CTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACC                                              <  SRR4302535.1781024/94‑1 (MQ=60)
                                                    GCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTC                                          >  SRR4302535.3928980/1‑94 (MQ=60)
                                                     CCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCA                                         >  SRR4302535.1137503/1‑94 (MQ=60)
                                                      CATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCAT                                        >  SRR4302535.855245/1‑94 (MQ=60)
                                                      CATTATTGCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCAT                                        <  SRR4302535.2146025/94‑1 (MQ=60)
                                                             GCCGACGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAA                                 <  SRR4302535.15008/94‑1 (MQ=60)
                                                                  CGATAAACGACCCAATCCCTGCACCGACAATAATCGCCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCC                            <  SRR4302535.3902803/94‑1 (MQ=60)
                                                                  CGATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCC                            >  SRR4302535.2741731/1‑94 (MQ=60)
                                                                    ATAAACGACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGA                          >  SRR4302535.2997807/1‑94 (MQ=60)
                                                                         CGACCCAATCCCTGCACCTACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACT                     <  SRR4302535.1428518/94‑1 (MQ=60)
                                                                         CGACACAATCCCTGCACCGGCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACT                     <  SRR4302535.935630/94‑1 (MQ=60)
                                                                          GACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTG                    <  SRR4302535.1224456/94‑1 (MQ=60)
                                                                           ACCCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGT                   >  SRR4302535.1411634/1‑94 (MQ=60)
                                                                             CCAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTAC                 <  SRR4302535.4518171/94‑1 (MQ=60)
                                                                              CAATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACC                <  SRR4302535.3840745/94‑1 (MQ=60)
                                                                              CAATCCCTGCACCAACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACC                >  SRR4302535.2550546/1‑94 (MQ=60)
                                                                               cacCCCTGCACCGCCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCG               <  SRR4302535.1145747/91‑1 (MQ=60)
                                                                               AATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCG               >  SRR4302535.668240/1‑94 (MQ=60)
                                                                                ATCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGA              >  SRR4302535.4130963/1‑94 (MQ=60)
                                                                                 TCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAG             <  SRR4302535.424679/94‑1 (MQ=60)
                                                                                 TCCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAG             <  SRR4302535.1650477/94‑1 (MQ=60)
                                                                                  CCCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGA            >  SRR4302535.2857868/1‑94 (MQ=60)
                                                                                   CCTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAA           >  SRR4302535.2466858/1‑94 (MQ=60)
                                                                                    CTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAAC          >  SRR4302535.4018714/1‑94 (MQ=60)
                                                                                    CTGCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAAC          <  SRR4302535.2467830/94‑1 (MQ=60)
                                                                                      GCACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAA        >  SRR4302535.3692625/1‑94 (MQ=60)
                                                                                        ACCGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACC      >  SRR4302535.332448/1‑94 (MQ=60)
                                                                                          CGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAG    <  SRR4302535.4515966/94‑1 (MQ=60)
                                                                                          CGACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAG    <  SRR4302535.55939/94‑1 (MQ=60)
                                                                                            ACAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAGGA  >  SRR4302535.881577/1‑94 (MQ=60)
                                                                                            |                                                                                             
TGGAGCGACGAAACAGCAACGGCAGCGCCTTCAGCGTGCCTTTAATCGCTTTGCCATTATTGCCGACGATAAACGACCCAATCCCTGCACCGGCAATAATCACCAGTTCAGCGGGTTGATAGAGTGCTCCAAGGCTTCCACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAGGT  >  NC_000913/1974959‑1975144

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑