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 I1 R1 300 54.7 1718999 98.4% 1691495 149.9

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_0009131,369,5200TC95.1% 138.2 / ‑6.3 41V43A (GTT→GCT) pspDperipheral inner membrane phage‑shock protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (9/30);  minor base A (2/0);  total (11/30)
Fisher's exact test for biased strand distribution p-value = 6.71e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑TTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAATTT  >  NC_000913/1369393‑1369666
                                                                                                                                |                                                                                                                                                    
aTGAATAATCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGGTAGGGGATTAAAACAG‑ACGATCGcccccc                                                                                                                                          >  1:253672/1‑136 (MQ=255)
          gCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGGCGGGGGGTAAAAACAA‑CTGCTCGCCGACCCCCGAAAAtttt                                                                                                                              >  2:661002/1‑142 (MQ=255)
             ggCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCtgtg                                                                                                                    <  2:160152/149‑1 (MQ=255)
                      ccGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAAcc                                                                                                       <  1:473939/151‑1 (MQ=255)
                        gggCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGc                                                                                                     <  1:202148/151‑1 (MQ=255)
                        gggCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGc                                                                                                     <  2:336181/151‑1 (MQ=255)
                            aaaaGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGCGGCGGGCTTGGTGCTTAAATTAC‑CTGCTCCCCGCCCCCGGAAAATTTTGCCGGCTGGGGC‑GCT‑GGaaactccgtt                                                                                                 >  2:63697/1‑143 (MQ=255)
                                 gTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTc                                                                                            <  2:404152/151‑1 (MQ=255)
                                      gCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGgct                                                                                       <  1:506760/151‑1 (MQ=255)
                                          ggTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGgctgct                                                                                    <  1:553833/150‑1 (MQ=255)
                                               cAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGGTGGGGGGTAAAAATAA‑CCGCTTGCCCACCCCTGGAAAAATTGGTGGGTGGGGCGGCT‑GG‑ACCCCCGTTTAATCGGGGTGGtaataa                                                                               >  2:42915/1‑150 (MQ=255)
                                               cAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCtaataa                                                                               <  2:14478/150‑1 (MQ=255)
                                                        aGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACC‑CTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGc                                                                    <  1:111047/151‑1 (MQ=255)
                                                         ggCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGc                                                                    <  1:209132/151‑1 (MQ=255)
                                                           cAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGGTGGGCGTTTAAATTAG‑ATTCCAGCCGACCACTGAAAAAATTTCTTGCTTTGGG‑GGC‑GGAACCCCTGTTTAGTCGGGCCGCTaaaaaaactgaac                                                                       >  2:781273/1‑139 (MQ=255)
                                                            aaGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGtt                                                                 <  1:411905/151‑1 (MQ=255)
                                                              gCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTtat                                                               <  2:309644/151‑1 (MQ=255)
                                                                      ttcttACCGCACTGCGCTATGGCCCGGCGGGGGTGGCGGGGTTGGGGGTAAAAAAAGACGGCTCCCCGCCCCCGGAAAAGGTTGTGGGGGGGGGG‑GCG‑GGAACCGCGGTTAATCGGGGCGGCT‑ATAAAATGGGCCCGCGGTTTaaaaaggg                                                       >  1:354704/1‑147 (MQ=255)
                                                                              gCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGGTAAAAACAG‑CTGCTCGCCCACCGCCGGAAAAGGTGGTGGGGGTGGC‑GCT‑GGGACCGCTGTTTAATCTGGGTGCTAATAAAACGGCACAGCGGTATAAAAAgggggggg                                                  >  1:240895/1‑148 (MQ=255)
                                                                                   gcgcTATGGCCCGGCGGGTGTGGCGGGGTTGGCGGTAAAAATAA‑CGGCTCGCCCACCGCCGGAAAAGTTTGTGGGTGGGGG‑GCTGGGAACGCCCGTTAA‑TCGGGCGGCCTATAAAATGGGACAGCGGTTTAAAAAgggggggggggtt                                             >  2:217488/1‑143 (MQ=255)
                                                                                   gcgcTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTc                                            <  1:136533/149‑1 (MQ=255)
                                                                                   gcgcTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCg                                           <  1:168261/150‑1 (MQ=255)
                                                                                        aTGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCaaa                                       <  2:283571/149‑1 (MQ=255)
                                                                                          ggCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAAtt                                   <  2:11337/151‑1 (MQ=255)
                                                                                            cccGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGt                                 <  1:619278/151‑1 (MQ=255)
                                                                                                      gtgGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCa                        <  1:229538/150‑1 (MQ=255)
                                                                                                      gtgGCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAg                       <  2:410819/151‑1 (MQ=255)
                                                                                                         gCGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCg                    <  2:776202/151‑1 (MQ=255)
                                                                                                          cGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGt                   <  1:781217/151‑1 (MQ=255)
                                                                                                          cGGGCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGt                   <  2:730730/151‑1 (MQ=255)
                                                                                                            ggCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGtat                 >  1:150633/1‑151 (MQ=255)
                                                                                                            ggCTGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGtat                 <  2:95560/151‑1 (MQ=255)
                                                                                                               tGGGCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAat              >  2:426239/1‑151 (MQ=255)
                                                                                                                gggCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGGTGTGGC‑GCT‑GGAACCGCTGTTAAGGCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGATGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATaa               <  1:15427/149‑1 (MQ=255)
                                                                                                                gggCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATaa               <  1:190201/149‑1 (MQ=255)
                                                                                                                gggCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAatg             <  2:210369/151‑1 (MQ=255)
                                                                                                                gggCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAat              <  1:14392/150‑1 (MQ=255)
                                                                                                                  gCGATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAatgg            >  1:390802/1‑150 (MQ=255)
                                                                                                                    gATAAAATCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAatggatg         <  2:240914/151‑1 (MQ=255)
                                                                                                                          aTCAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAAtt   <  1:187829/151‑1 (MQ=255)
                                                                                                                            cAG‑CTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAAttt  <  1:597388/150‑1 (MQ=255)
                                                                                                                                |                                                                                                                                                    
ATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAG‑TTGCTCGCCGACCGCTGAAAATGTTGCTGGCTGTGGC‑GCT‑GGAACCGCTGTTAAGTCGGGCTGCTAATAAACTGGCACAGCGTTATAAAAGGTGAGGGGAGTTTCGCAAAAATTGTTAAATCTCAGGCGTATAATGGATGGCAATTT  >  NC_000913/1369393‑1369666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A