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
A3 F28 I1 R1 146 75.3 2562504 98.6% 2526628 139.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,240,984 (G)7→8 coding (1041/1245 nt) sstT → serine/threonine:Na(+) symporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,240,9771.G92.9% 93.8 / 0.8 28coding (1034/1245 nt)sstTserine/threonine:Na(+) symporter
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base G (1/25);  total (2/26)
Fisher's exact test for biased strand distribution p-value = 1.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

GCGGGCGCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAACCGCGCTGAA  >  NC_000913/3240844‑3241106
                                                                                                                                      |                                                                                                                                  
gctggcgCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑gggggg                                                                                                                             >  2:913453/4‑140 (MQ=255)
 cgggcgCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGGTCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑ggggggg                                                                                                                            <  2:46262/140‑1 (MQ=255)
    gcgcAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑gggggggggt                                                                                                                         <  1:124901/140‑4 (MQ=255)
      gcagcaATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑ggggggggtctc                                                                                                                       <  1:787865/140‑6 (MQ=255)
           aaTCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTctgctg                                                                                                                   <  1:983396/140‑1 (MQ=255)
                cTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGTCTCTGCTGCTGa                                                                                                               <  1:1172063/140‑1 (MQ=255)
                cTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGTCTCTGCTGCTGa                                                                                                               <  1:850210/140‑1 (MQ=255)
                  aTTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATcc                                                                                                            >  1:632062/1‑140 (MQ=255)
                    tACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCa                                                                                                          <  2:1224133/140‑1 (MQ=255)
                    tACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCa                                                                                                          <  1:873416/140‑1 (MQ=255)
                      ccGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACt                                                                                                        <  1:366033/140‑1 (MQ=255)
                      ccGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACt                                                                                                        <  1:936956/140‑1 (MQ=255)
                       cGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTg                                                                                                       >  2:1010177/1‑140 (MQ=255)
                       cGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTg                                                                                                       <  1:283129/140‑1 (MQ=255)
                       cGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTGCTGCTGATCCCAccg                                                                                                       >  1:40441/1‑138 (MQ=255)
                         tgtTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGc                                                                                                     >  2:342324/1‑140 (MQ=255)
                         tgtTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTGCTGCTGGTCCCCCCGGc                                                                                                     >  2:663752/1‑140 (MQ=255)
                           ttGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTGCTGCTGATCCCCCCGGccc                                                                                                   >  2:334443/1‑139 (MQ=255)
                                   ggctgCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATg                                                                                           >  1:914194/1‑140 (MQ=255)
                                     ctgCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTGCTGCTGATCCCCCTTGCCCGTAATATGtt                                                                                         >  1:1184276/1‑140 (MQ=255)
                                                 cGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGaa                                                                             <  2:632062/140‑1 (MQ=255)
                                                       gTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGatat                                                                       <  1:630032/140‑1 (MQ=255)
                                                       gTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGatat                                                                       <  2:558515/140‑1 (MQ=255)
                                                       gTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGatat                                                                       <  1:1034657/140‑1 (MQ=255)
                                                         aTTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCg                                                                     <  2:710779/140‑1 (MQ=255)
                                                          ttCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGGCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCg                                                                     >  1:237890/1‑140 (MQ=255)
                                                              ggTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATg                                                                <  1:663752/140‑1 (MQ=255)
                                                                           aCGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCg                                                   <  2:685420/140‑1 (MQ=255)
                                                                             ggCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTTCTTCTGATCCCCCTGGCCCGTAATATTTTTTGGATTTTGAACGATATCGCCCTGCAGGGGGGTTCCGtt                                                 >  2:280441/1‑139 (MQ=255)
                                                                              gcgcTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTTCTGCTGATCCCACCGGCCCGTAAAATGTTCCGTATTTTGGACGGTATCTCCCTGGAGGGGGGTGCCggcc                                                >  2:917366/1‑137 (MQ=255)
                                                                                   gctgTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCttt                                           <  1:866602/140‑1 (MQ=255)
                                                                                       ttGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑GGGGGGGGCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTatcat                                      >  2:443593/1‑140 (MQ=255)
                                                                                        tGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTatcat                                      <  1:808698/140‑1 (MQ=255)
                                                                                        tGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTatcat                                      <  1:342324/140‑1 (MQ=255)
                                                                                           gCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCg                                    <  1:474512/140‑1 (MQ=255)
                                                                                            cGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGc                                  <  1:1010177/140‑1 (MQ=255)
                                                                                            cGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCg                                 <  1:443593/140‑1 (MQ=255)
                                                                                              tggtggCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGGCTCTTCTGCTGATCCCACCGGCCTGTAATATGTTCGGGATTTCGAACGATATCGCCATGCAGGGGGGTGCCGGCGGCTTTTTTATCgggg                                 >  2:474512/1‑138 (MQ=255)
                                                                                                        tctGTGTGCCTGTGGCGCATCCGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGAc                      <  1:334443/140‑1 (MQ=255)
                                                                                                         ctGTGTGCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGAc                      <  1:890234/140‑1 (MQ=255)
                                                                                                          tgtgtgCCTGTGGCGCATCCGGCGTGGCGGGGGGGGGGCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGGATTTCGAACGGTATCGCCCTGCCGGGGGGTGCCGTCGGCTTTTTCATCGGCGTATTGCAGGAcc                     >  2:648421/1‑139 (MQ=255)
                                                                                                                  tgtgGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGGGGGTGCCGGCGGCTTTTTCATCGGCGTATTGCAGGACTCTTGCGaaa            >  2:764971/1‑140 (MQ=255)
                                                                                                                   gtgGCGCATCCGGCGTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGaaa            <  1:648421/140‑1 (MQ=255)
                                                                                                                    tgGCGCATCCGGCGTGGCG‑GGGGGGGGCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGGATTTCGAACGATATCGCCCTGCAGGGGGGTGCCGTCGGCTTTTTTATCGGCGTATTGCAGGACTCTTTCGAAAcc          >  2:779342/1‑140 (MQ=255)
                                                                                                                           tCCGGCGTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAACCGCGCTg    <  1:306387/140‑1 (MQ=255)
                                                                                                                            ccGGCGTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAACCGCGCTGaa  <  1:913453/140‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                  
GCGGGCGCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGCGTGGC‑‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAACCGCGCTGAA  >  NC_000913/3240844‑3241106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A