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
A6 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,019,797 T→C 57.1% Y249C (TAT→TGT)  uidC ← predicted outer membrane porin protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,019,7970TC57.1% 27.7 / 77.0 63Y249C (TAT→TGT) uidCpredicted outer membrane porin protein
Reads supporting (aligned to +/- strand):  ref base T (17/10);  new base C (15/21);  total (32/31)
Fisher's exact test for biased strand distribution p-value = 1.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.78e-01

GCTGGCTGGTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTGTACCG  >  minE/1019729‑1019866
                                                                    |                                                                     
gctggctgGTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATaa                                                                     >  1:3649677/1‑71 (MQ=255)
    gctggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAAtt                                                                   <  1:2220009/69‑1 (MQ=255)
     ctggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCgg                                                                <  1:2286086/71‑1 (MQ=255)
      tggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCgg                                                                <  1:2595237/70‑1 (MQ=255)
       ggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAG‑AACTCCCCTTTCAACGTACAATTCGGGTc                                                             >  1:2092223/1‑71 (MQ=255)
           ttACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAg                                                          <  1:2831286/71‑1 (MQ=255)
           ttACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAg                                                          <  1:809187/71‑1 (MQ=255)
            tACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAg                                                          <  1:2534458/70‑1 (MQ=255)
            tACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGc                                                         >  1:1628421/1‑71 (MQ=255)
             aCGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCg                                                        >  1:1854106/1‑71 (MQ=255)
              cGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCg                                                        <  1:1933475/70‑1 (MQ=255)
              cGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCg                                                        <  1:30786/70‑1 (MQ=255)
              cGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       <  1:2210368/71‑1 (MQ=255)
              cGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       <  1:1060070/71‑1 (MQ=255)
               gACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       <  1:649895/70‑1 (MQ=255)
                aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTa                                                     >  1:3600770/1‑71 (MQ=255)
                aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       >  1:2324727/1‑69 (MQ=255)
                aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       >  1:3453046/1‑69 (MQ=255)
                aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTa                                                     <  1:2409716/71‑1 (MQ=255)
                aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTa                                                     <  1:1982891/71‑1 (MQ=255)
                 cTTAAACCTTCGAGCTGCGAGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTAt                                                    >  1:2626501/1‑71 (MQ=255)
                    aaaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATg                                                   <  1:2099307/69‑1 (MQ=255)
                    aaaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGc                                                  <  1:1546340/70‑1 (MQ=255)
                    aaaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCt                                                 >  1:3181398/1‑71 (MQ=255)
                     aaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCtt                                                <  1:1354135/71‑1 (MQ=255)
                     aaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCtt                                                <  1:1384971/71‑1 (MQ=255)
                       ccTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCtttt                                              >  1:3332856/1‑71 (MQ=255)
                       ccTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCtttt                                              <  1:2836429/71‑1 (MQ=255)
                          tCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTtctc                                           >  1:2022815/1‑71 (MQ=255)
                           cGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTtct                                            <  1:286971/69‑1 (MQ=255)
                            gAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       >  1:49127/1‑57 (MQ=255)
                            gAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                       >  1:451588/1‑57 (MQ=255)
                               cTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGt                                                      <  1:1998680/55‑1 (MQ=255)
                               cTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGt                                                      <  1:871911/55‑1 (MQ=255)
                               cTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGaa                                      >  1:2849894/1‑71 (MQ=255)
                                      tAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTg                               >  1:2340466/1‑71 (MQ=255)
                                        aaaGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTa                             >  1:470783/1‑71 (MQ=255)
                                        aaaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCg                                                            <  1:3034856/40‑1 (MQ=255)
                                        aaaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATAc                                   <  1:3285622/65‑1 (MQ=255)
                                         aaGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGt                                                      <  1:3406436/45‑1 (MQ=255)
                                          aGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATc                           >  1:729289/1‑71 (MQ=255)
                                          aGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATAc                                   <  1:2417110/63‑1 (MQ=255)
                                          aGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACttt                                <  1:1896183/66‑1 (MQ=255)
                                          aGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACttt                                <  1:1914659/66‑1 (MQ=255)
                                                  aaCTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTgg                    >  1:1205350/1‑70 (MQ=255)
                                                  aaCTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTgg                    >  1:2780985/1‑70 (MQ=255)
                                                    cTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCga                                         <  1:1430437/47‑1 (MQ=255)
                                                      ccccTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCgaga                                       >  1:3124333/1‑47 (MQ=255)
                                                      ccccTTTCAACGTATAATTCGGCTCGAGCGGTATGCTTTTCTCgaga                                       >  1:2798339/1‑47 (MQ=255)
                                                      ccccTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACa               >  1:2084128/1‑71 (MQ=255)
                                                       cccTTTCAACGTATAATTCGGGTCGAGCGGTATGCt                                                 <  1:1905974/36‑1 (MQ=255)
                                                         cTTTCAACGTATAATTCGGGTCGAGCGGTATGCttt                                               >  1:3165543/1‑36 (MQ=255)
                                                         cTTTCAACGTATAATTCGGGTCGAGCGGTATGCttt                                               >  1:2004371/1‑36 (MQ=255)
                                                         cTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCt            >  1:957375/1‑71 (MQ=255)
                                                          tttCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACtt                                 >  1:924889/1‑49 (MQ=255)
                                                          tttCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCtt           >  1:503833/1‑71 (MQ=255)
                                                            tCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCga                                         >  1:1575813/1‑39 (MQ=255)
                                                            tCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCga                                         >  1:1244738/1‑39 (MQ=255)
                                                             cAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCt        >  1:2462248/1‑71 (MQ=255)
                                                             cAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCt        >  1:1954878/1‑71 (MQ=255)
                                                               aCGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTg       <  1:3154245/70‑1 (MQ=255)
                                                                cGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACt                                  <  1:3486623/42‑1 (MQ=255)
                                                                 gTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATATTTCTGTa     >  1:3099202/1‑70 (MQ=255)
                                                                    taATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTGTACCg  <  1:338987/70‑1 (MQ=255)
                                                                    taATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTGTACCg  <  1:1383371/70‑1 (MQ=255)
                                                                    |                                                                     
GCTGGCTGGTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTGTACCG  >  minE/1019729‑1019866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A