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 1,847,298 A→G K146K (AAA→AAG sppA → protease IV

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,847,2980AG99.1% 323.5 / NA 106K146K (AAA→AAGsppAprotease IV
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (48/57);  minor base T (0/1);  total (48/58)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 110 total aligned reads displayed.

TGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAACCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGT  >  NC_000913/1847208‑1847387
                                                                                          |                                                                                         
tgtgATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGcc                                                                                         <  1:772100/93‑1 (MQ=255)
 gtgATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCg                                                                                        >  2:595710/1‑93 (MQ=255)
  tgATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCgg                                                                                       >  2:486103/1‑93 (MQ=255)
   gATGGATCTGAAAAACTTCGCAGGCGGCGATCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCATGACAGCGGGAATCCGGt                                                                                      <  2:156293/93‑1 (MQ=255)
   gATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGt                                                                                      >  2:4428743/1‑93 (MQ=255)
   gATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGt                                                                                      >  1:2799056/1‑93 (MQ=255)
    aTGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGtt                                                                                     <  1:417471/93‑1 (MQ=255)
    aTGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGtt                                                                                     >  1:118999/1‑93 (MQ=255)
    aTGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGtt                                                                                     <  1:4298971/93‑1 (MQ=255)
    aTGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGtt                                                                                     <  2:4331001/93‑1 (MQ=255)
    aTGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGtt                                                                                     <  1:369140/93‑1 (MQ=255)
     tGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGttt                                                                                    <  2:4366124/93‑1 (MQ=255)
      taaTCTGAAAAACTTCGCAGGCGGCGACCAACCATCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTa                                                                                   <  1:813832/91‑1 (MQ=255)
      ggATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTa                                                                                   <  2:2638822/93‑1 (MQ=255)
       gATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTAt                                                                                  <  1:3880286/93‑1 (MQ=255)
       gATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTAt                                                                                  <  1:232110/93‑1 (MQ=255)
         tCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGc                                                                                >  2:752088/1‑93 (MQ=255)
         tCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGc                                                                                >  1:1567957/1‑93 (MQ=255)
         tCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGc                                                                                <  2:951913/93‑1 (MQ=255)
         tCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGATTCGTGACAGCGGGAAGCCGGTTTATGc                                                                                >  1:1913474/1‑93 (MQ=255)
          cTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGGAGCCGGTTTATGcc                                                                               >  2:222649/1‑93 (MQ=255)
          cTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGcc                                                                               <  1:1843318/93‑1 (MQ=255)
          cTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGcc                                                                               <  1:4621045/93‑1 (MQ=255)
            gAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGt                                                                             >  2:4542169/1‑93 (MQ=255)
             aaaaaCTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGtt                                                                            <  2:448515/93‑1 (MQ=255)
             aaaaaCTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGtt                                                                            >  2:1909962/1‑93 (MQ=255)
              aaaaCTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTg                                                                           <  1:1111648/93‑1 (MQ=255)
              aaaaCTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTg                                                                           <  2:4527447/93‑1 (MQ=255)
               aaaCCTCGCAGGCGGCGGCCACCCGTCTGTGCAGTACATCGGCAAAGCTCTGAAGGAGTTTCGTGACAGCGGGAAGGCGGTTTATGCCGTTgg                                                                          <  2:4022872/93‑1 (MQ=255)
                aaCTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGc                                                                         >  1:588608/1‑93 (MQ=255)
                  cTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCga                                                                       <  2:775013/93‑1 (MQ=255)
                  cTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCga                                                                       <  1:14244/93‑1 (MQ=255)
                  cTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCga                                                                       <  1:2929715/93‑1 (MQ=255)
                  cTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCga                                                                       <  2:769372/93‑1 (MQ=255)
                    tCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCgaga                                                                     <  1:3818507/93‑1 (MQ=255)
                     cGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGaa                                                                    <  2:954175/93‑1 (MQ=255)
                      gCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAAc                                                                   >  1:1820345/1‑93 (MQ=255)
                         ggcggcGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTAc                                                                <  2:2449962/93‑1 (MQ=255)
                          gcggcgACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACa                                                               <  2:2524908/93‑1 (MQ=255)
                          gcggcgACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACa                                                               <  1:2818056/93‑1 (MQ=255)
                          gcggcgACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACa                                                               <  1:3101290/93‑1 (MQ=255)
                            ggcgACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGc                                                             <  1:3636895/93‑1 (MQ=255)
                              cgACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCa                                                           <  1:3857076/93‑1 (MQ=255)
                              cgACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCa                                                           <  2:3819441/93‑1 (MQ=255)
                                aCCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAgg                                                         <  2:3455026/93‑1 (MQ=255)
                                 ccAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAggg                                                        >  1:2120593/1‑93 (MQ=255)
                                 ccAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGCTTATGCCGTTGGCGAGAACTACAGCCAggg                                                        >  1:2120592/1‑93 (MQ=255)
                                   aaCCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGc                                                      >  1:3660390/1‑93 (MQ=255)
                                    aCCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCa                                                     >  1:3500405/1‑93 (MQ=255)
                                     ccGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCaa                                                    <  1:3174543/93‑1 (MQ=255)
                                       gTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAata                                                  <  2:3334867/93‑1 (MQ=255)
                                        tCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAatat                                                 >  1:594100/1‑93 (MQ=255)
                                        tCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAatat                                                 >  1:4174108/1‑93 (MQ=255)
                                        tCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAatat                                                 >  2:2632144/1‑93 (MQ=255)
                                            tGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTAtc                                             >  2:180185/1‑93 (MQ=255)
                                             gCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTAtct                                            >  2:154708/1‑93 (MQ=255)
                                             gCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTAtct                                            >  1:383623/1‑93 (MQ=255)
                                             gCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTAtct                                            >  2:960611/1‑93 (MQ=255)
                                              cAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTAtctc                                           <  2:1079331/93‑1 (MQ=255)
                                              cAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTAtctc                                           >  1:3730781/1‑93 (MQ=255)
                                               aGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCg                                          <  1:1487143/93‑1 (MQ=255)
                                                gTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGc                                         >  1:583902/1‑93 (MQ=255)
                                                atACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGc                                         <  1:413838/92‑1 (MQ=255)
                                                  aCATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCa                                       >  1:1173255/1‑93 (MQ=255)
                                                    aTCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGt                                     >  1:1483010/1‑93 (MQ=255)
                                                    aTCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGt                                     <  1:2016984/93‑1 (MQ=255)
                                                    aTCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGt                                     >  2:3012433/1‑93 (MQ=255)
                                                    aTCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGt                                     >  2:4333822/1‑93 (MQ=255)
                                                     tCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGtt                                    >  1:771277/1‑93 (MQ=255)
                                                     tCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGtt                                    >  1:2837176/1‑93 (MQ=255)
                                                      cGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGttt                                   >  1:2837135/1‑93 (MQ=255)
                                                      cGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGttt                                   <  1:870036/93‑1 (MQ=255)
                                                      cGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGttt                                   <  2:339005/93‑1 (MQ=255)
                                                       ggCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTc                                  >  1:2202490/1‑93 (MQ=255)
                                                       ggCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTc                                  <  2:2815241/93‑1 (MQ=255)
                                                         cAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGc                                <  2:335087/93‑1 (MQ=255)
                                                          aaaGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGcc                               <  2:1736477/93‑1 (MQ=255)
                                                           aaGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCa                              >  1:1281588/1‑93 (MQ=255)
                                                               tctGAAAGAGTTGCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATaa                          <  2:4402258/93‑1 (MQ=255)
                                                                  gAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAAt                       <  1:2511709/93‑1 (MQ=255)
                                                                    aaGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAAttt                     >  1:1505458/1‑93 (MQ=255)
                                                                    aaGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAAttt                     >  1:632816/1‑93 (MQ=255)
                                                                    aaGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAAttt                     >  1:3139796/1‑93 (MQ=255)
                                                                      gagTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTgg                   >  1:468767/1‑93 (MQ=255)
                                                                       agTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGc                  >  2:4554488/1‑93 (MQ=255)
                                                                        gTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCt                 <  2:3580719/93‑1 (MQ=255)
                                                                        gTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCt                 >  1:3720851/1‑93 (MQ=255)
                                                                        gTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCt                 >  2:2445522/1‑93 (MQ=255)
                                                                         tttCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTg                >  2:4279691/1‑93 (MQ=255)
                                                                           tCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGtc              >  2:2479292/1‑93 (MQ=255)
                                                                            cGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGtct             >  2:3950771/1‑93 (MQ=255)
                                                                             gTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGtctc            <  2:2668589/93‑1 (MQ=255)
                                                                              tGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTcc           <  2:907984/93‑1 (MQ=255)
                                                                               gACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCg          >  1:1534278/1‑93 (MQ=255)
                                                                               gACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCg          >  2:921945/1‑93 (MQ=255)
                                                                                  aGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCaa       <  2:2672253/93‑1 (MQ=255)
                                                                                  aGCGGGAAGCCGGTTTATGCCGTCGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCaa       <  1:3571283/93‑1 (MQ=255)
                                                                                   gCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAg      <  1:2103052/93‑1 (MQ=255)
                                                                                      ggAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCg   <  1:2788/93‑1 (MQ=255)
                                                                                       gAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGt  <  2:3024485/93‑1 (MQ=255)
                                                                                          |                                                                                         
TGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAACCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGT  >  NC_000913/1847208‑1847387

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ 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
ATTGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAACCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGTGG  >  NC_000913/1847206‑1847389
                                                                                            |                                                                                           
ATTGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGC                                                                                            <  SRR4302535.1142717/94‑1 (MQ=60)
ATTGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGC                                                                                            >  SRR4302535.680915/1‑94 (MQ=60)
  TGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCG                                                                                          <  SRR4302535.777533/94‑1 (MQ=60)
    TGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGT                                                                                        >  SRR4302535.2818973/1‑94 (MQ=60)
     GATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTT                                                                                       >  SRR4302535.119831/1‑94 (MQ=60)
      ATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTT                                                                                      <  SRR4302535.420397/94‑1 (MQ=60)
      ATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTT                                                                                      <  SRR4302535.371688/94‑1 (MQ=60)
      ATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTT                                                                                      <  SRR4302535.4328393/94‑1 (MQ=60)
        taATCTGAAAAACTTCGCAGGCGGCGACCAACCATCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTAT                                                                                    <  SRR4302535.819540/92‑1 (MQ=60)
         GATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATG                                                                                   <  SRR4302535.3906920/94‑1 (MQ=60)
         GATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATG                                                                                   <  SRR4302535.233713/94‑1 (MQ=60)
          ATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGC                                                                                  >  SRR4302535.1579273/1‑94 (MQ=60)
          ATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGATTCGTGACAGCGGGAAGCCGGTTTATGC                                                                                  >  SRR4302535.1927264/1‑94 (MQ=60)
            CTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCG                                                                                <  SRR4302535.4652441/94‑1 (MQ=60)
            CTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCG                                                                                <  SRR4302535.1856611/94‑1 (MQ=60)
                AAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGG                                                                            <  SRR4302535.1119582/94‑1 (MQ=60)
                AAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGG                                                                            <  SRR4302535.3587190/94‑1 (MQ=60)
                 AAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGC                                                                           >  SRR4302535.592736/1‑94 (MQ=60)
                 AAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGC                                                                           <  SRR4302535.2690519/94‑1 (MQ=60)
                    CTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAG                                                                        >  SRR4302535.4127432/1‑94 (MQ=60)
                    CTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAG                                                                        <  SRR4302535.14345/94‑1 (MQ=60)
                    CTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAG                                                                        <  SRR4302535.2950354/94‑1 (MQ=60)
                      TCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAA                                                                      <  SRR4302535.3844856/94‑1 (MQ=60)
                       CGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAAC                                                                     >  SRR4302535.1833495/1‑94 (MQ=60)
                           GGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACA                                                                 <  SRR4302535.1589008/94‑1 (MQ=60)
                            GCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAG                                                                <  SRR4302535.2838074/94‑1 (MQ=60)
                            GCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAG                                                                <  SRR4302535.3122879/94‑1 (MQ=60)
                              GGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCC                                                              <  SRR4302535.3662098/94‑1 (MQ=60)
                                CGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAG                                                            <  SRR4302535.3883629/94‑1 (MQ=60)
                                  ACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGG                                                          >  SRR4302535.2135887/1‑94 (MQ=60)
                                  ACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGCTTATGCCGTTGGCGAGAACTACAGCCAGGG                                                          >  SRR4302535.2135886/1‑94 (MQ=60)
                                    CAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGC                                                        >  SRR4302535.3685726/1‑94 (MQ=60)
                                     AACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCA                                                       >  SRR4302535.3524742/1‑94 (MQ=60)
                                      ACCTTCTATGCAGTACATCGACAAGGCTCTGAAAGAGTTTCGTGACAGCGGAAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAA                                                      <  SRR4302535.686553/94‑1 (MQ=60)
                                       CCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAAT                                                     <  SRR4302535.3196512/94‑1 (MQ=60)
                                         GTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATAT                                                   >  SRR4302535.598265/1‑94 (MQ=60)
                                         GTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATAT                                                   >  SRR4302535.4202675/1‑94 (MQ=60)
                                              TGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCT                                              >  SRR4302535.386281/1‑94 (MQ=60)
                                               GCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTC                                             >  SRR4302535.3756615/1‑94 (MQ=60)
                                                 AGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGC                                           >  SRR4302535.587997/1‑94 (MQ=60)
                                                 AGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGC                                           <  SRR4302535.1497793/94‑1 (MQ=60)
                                                  ATACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCC                                          <  SRR4302535.416744/94‑1 (MQ=60)
                                                   TACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCA                                         >  SRR4302535.1181632/1‑94 (MQ=60)
                                                     CATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGT                                       >  SRR4302535.1493615/1‑94 (MQ=60)
                                                      ATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTT                                      >  SRR4302535.2857310/1‑94 (MQ=60)
                                                      ATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTT                                      <  SRR4302535.2031512/94‑1 (MQ=60)
                                                      ATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTT                                      >  SRR4302535.776706/1‑94 (MQ=60)
                                                       TCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTT                                     >  SRR4302535.2857269/1‑94 (MQ=60)
                                                        CGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTC                                    <  SRR4302535.876200/94‑1 (MQ=60)
                                                        CGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTC                                    >  SRR4302535.2218187/1‑94 (MQ=60)
                                                            AAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCA                                >  SRR4302535.1290734/1‑94 (MQ=60)
                                                                    GAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATT                        <  SRR4302535.2529814/94‑1 (MQ=60)
                                                                    GAAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGAGAGACCTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATT                        <  SRR4302535.2790035/94‑1 (MQ=60)
                                                                     AAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTT                       >  SRR4302535.3161644/1‑94 (MQ=60)
                                                                     AAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTT                       >  SRR4302535.637224/1‑94 (MQ=60)
                                                                     AAAGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTT                       >  SRR4302535.1516281/1‑94 (MQ=60)
                                                                       AGAGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGG                     >  SRR4302535.472048/1‑94 (MQ=60)
                                                                         AGTTTCGTGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCT                   >  SRR4302535.3746628/1‑94 (MQ=60)
                                                                                TGACAGCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCG            >  SRR4302535.1545331/1‑94 (MQ=60)
                                                                                    AGCGGGAAGCCGGTTTATGCCGTCGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAG        <  SRR4302535.3596048/94‑1 (MQ=60)
                                                                                     GCGGGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGG       <  SRR4302535.2118220/94‑1 (MQ=60)
                                                                                        GGAAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGT    <  SRR4302535.2813/94‑1 (MQ=60)
                                                                                          AAGCCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGTGG  <  SRR4302535.3505608/94‑1 (MQ=60)
                                                                                            |                                                                                           
ATTGTGATGGATCTGAAAAACTTCGCAGGCGGCGACCAACCGTCTATGCAGTACATCGGCAAAGCTCTGAAAGAGTTTCGTGACAGCGGGAAACCGGTTTATGCCGTTGGCGAGAACTACAGCCAGGGGCAATATTATCTCGCCAGTTTCGCCAATAAAATTTGGCTGTCTCCGCAAGGCGTGG  >  NC_000913/1847206‑1847389

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: