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 F50 I2 R1 257 49.9 1554294 99.0% 1538751 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,369,520 T→C V43A (GTT→GCT)  pspD → peripheral inner membrane phage‑shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,369,5200TC97.6% 130.5 / NA 41V43A (GTT→GCT) pspDperipheral inner membrane phage‑shock protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (11/29);  minor base G (1/0);  total (12/29)
Fisher's exact test for biased strand distribution p-value = 2.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGTTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAATT  >  NC_000913/1369388‑1369665
                                                                                                                                     |                                                                                                                                                   
aaGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGTGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGaa                                                                                                                                   <  2:79329/151‑1 (MQ=255)
aaGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGaa                                                                                                                                   <  2:659306/151‑1 (MQ=255)
 aGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGGCGGGGGTGGGCG‑TAAAAACAAGCGCTCCCCGAcccccgg                                                                                                                                    >  1:536368/1‑144 (MQ=255)
    tATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGGTAAAAATAGCTTCTCCCCGACCGCCGgaaa                                                                                                                                 >  2:224553/1‑149 (MQ=255)
               gCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGGGGGGGGGGAAAAACAGCCGCTCGCCCCCCGCCGGAAAAGGTgctgg                                                                                                                        >  1:181168/1‑147 (MQ=255)
                                cAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGGGGTAAAAATAACTGCTCGCCCCCCCCTGGAAATTTTTCTGGCCGTGGGG‑CTTGGAcccccgt                                                                                                  >  2:295539/1‑146 (MQ=255)
                                 aaaaGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGGG‑GGGCTGGGGGGTAAAATTACCAGCTCGCCCGCCGCTGGAAAAGTTTGTGGGGTTGGGG‑CTGGGAGCGCCGtt                                                                                                 >  2:759838/1‑151 (MQ=255)
                                 aaaaGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGATGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGtt                                                                                                 <  2:184860/151‑1 (MQ=255)
                                               ggTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGgctgct                                                                                    <  2:703665/150‑1 (MQ=255)
                                                   tCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCtaata                                                                                <  2:563682/150‑1 (MQ=255)
                                                        ttAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGGCGGGGGGTAAAAAAAACCGCTCCCCGCCCGCTGAAAAAGTTGCTGGCTGTGGGG‑CTGGGACCGCCGTTTAATCGGGGTGGTAATaaaattg                                                                          >  1:88332/1‑147 (MQ=255)
                                                              ggCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGc                                                                    <  1:352101/151‑1 (MQ=255)
                                                               gCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑g                                                                  <  1:594174/151‑1 (MQ=255)
                                                                      ggTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATaaa                                                           <  1:541468/151‑1 (MQ=255)
                                                                          cttcttACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAgg                                                        <  1:473404/150‑1 (MQ=255)
                                                                            tcttACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTg                                                      <  1:350544/150‑1 (MQ=255)
                                                                             cttACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGGGGTAAAAACAGCTGCTCCCCCACCGCTGGAAAAGGTGCTGGGTGTGGGGCCGGGAACCCCGGTTAA‑TCGGGGTGCTAATAAAATGGGGCAGC‑GTTATaaaaaggg                                                      >  2:337505/1‑145 (MQ=255)
                                                                             cgtACCGCACTGCGCTATGGGCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTGGCCGACCGCGGAAAAGGTTGCTGGCGGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAg                                                    <  1:602024/149‑1 (MQ=255)
                                                                               tACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGa                                                     <  2:400910/148‑1 (MQ=255)
                                                                               tACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAgg                                                   <  1:653033/150‑1 (MQ=255)
                                                                               tACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAg                                                    <  2:101842/149‑1 (MQ=255)
                                                                                 ccGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGGGGTAAAAAAAGCCGCTCGCCCCCCGCCGGAAAAGTTTTTGGGTGGGGGG‑CCGGGACCGCTGTTTAGTCGGGGTGCTAATAAAATGGGACAGCGGTTTTAAAAGgggggggg                                                 >  1:650506/1‑151 (MQ=255)
                                                                                    cACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGtt                                             <  2:757361/151‑1 (MQ=255)
                                                                                        gcgcTATGGCCCGGCGGGTGTGGC‑GGGGCGGGCGATAAAAACAGCCTCTCGCCCACCCCCGGAAAAGTTGCTGGGGGGGGGG‑CCGGGAACGCTGGTTAGTCGGGCCGCTAATAAAATTGCACAGC‑CTTTTTAAAAGGGAgggggggtt                                            >  1:367650/1‑143 (MQ=255)
                                                                                        gcgcTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGTCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCg                                          <  1:104145/150‑1 (MQ=255)
                                                                                        gcgcTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCg                                          <  1:56568/150‑1 (MQ=255)
                                                                                               ggCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAAtt                                  <  2:38907/151‑1 (MQ=255)
                                                                                                 cccGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGt                                <  2:293914/151‑1 (MQ=255)
                                                                                                  ccGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCAGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGtt                               <  1:31765/151‑1 (MQ=255)
                                                                                                   cggcggGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTa                              <  1:535288/151‑1 (MQ=255)
                                                                                                      cggGTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAAt                           <  2:650564/151‑1 (MQ=255)
                                                                                                       gggTGTGGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCCACCGCTGGAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTTAATCGGGCTGCTAATAAAATGGCACAGC‑GTTATAAAAGGGGAGGGGAGGTTCGCAAAAAATGTTAAAt                           >  1:288674/1‑150 (MQ=255)
                                                                                                           gtgGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAg                      <  1:107336/151‑1 (MQ=255)
                                                                                                            tgGC‑GGGCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAgg                     >  1:360575/1‑151 (MQ=255)
                                                                                                                 gggCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGta                 <  2:146623/151‑1 (MQ=255)
                                                                                                                  ggCTGGGCGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGtat                <  2:722106/151‑1 (MQ=255)
                                                                                                                         cGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAatggat         >  1:85221/1‑151 (MQ=255)
                                                                                                                         cGATAAAATCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAatggat         <  2:73071/151‑1 (MQ=255)
                                                                                                                             aaaaTCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGc      <  2:577024/150‑1 (MQ=255)
                                                                                                                               aaTCAGCTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAAt   <  1:530443/151‑1 (MQ=255)
                                                                                                                                aTCAGCTGCGCGCCGACCGCTGAAAATGATGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑TATATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATCATGGATGGCCAtt  <  1:416698/151‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                                   
AAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGC‑GGGCTGGGCGATAAAATCAGTTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGCG‑CTGGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGC‑GTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAATT  >  NC_000913/1369388‑1369665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A