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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,707,029 A→G V37V (GTA→GTG)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,707,0290AG97.5% 130.5 / ‑4.1 40V37V (GTA→GTG) rsxCSoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (19/20);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

TCTGCATTCAGAAAAAATAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTACCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTATTGCGCGGCC  >  NC_000913/1706934‑1707123
                                                                                               |                                                                                              
tctGCATTCAGAAAAAATAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGcccc                                                                                            <  1:1000983/100‑1 (MQ=255)
tctGCATTCAGAAAAAATAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGcccc                                                                                            <  1:555621/100‑1 (MQ=255)
     aTTCAGAAAAAATAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGgcg                                                                                       <  2:1531025/100‑1 (MQ=255)
      ttCAGAAAAAATAAAATCTGGGCTTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGgcgc                                                                                      <  1:499756/100‑1 (MQ=255)
       tCAGAAAAAATAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCa                                                                                     <  1:1007314/100‑1 (MQ=255)
           aaaaaaTAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACTCATGCCAACGGTACTCCCCTGCGCCAGGGGCACCTGGCGCAgggg                                                                                 <  2:1337982/100‑4 (MQ=255)
              aaataaaatCTGGGATTTCAACCGCGGCATCCATCCAGCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGtttt                                                                              <  2:1063383/100‑1 (MQ=255)
                 taaaatCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGtt                                                                           <  1:120444/100‑1 (MQ=255)
                   aaatCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTAt                                                                         >  1:1576053/1‑100 (MQ=255)
                     gacTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTc                                                                       <  1:486472/98‑1 (MQ=255)
                     atCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTc                                                                       >  2:1313424/1‑100 (MQ=255)
                      tCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTcc                                                                      >  1:600438/1‑100 (MQ=255)
                         gggATTTCAACGGCGGCATCCATCCTCCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCAc                                                                    <  1:441004/99‑1 (MQ=255)
                         gggATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACt                                                                   >  1:1034557/1‑100 (MQ=255)
                          ggATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTg                                                                  <  1:974962/100‑1 (MQ=255)
                             tttCAACGGCGGCATCCATCCACCGGAGCTGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGaaa                                                               >  1:942982/1‑100 (MQ=255)
                              ttCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAAc                                                              <  2:399436/100‑1 (MQ=255)
                               tCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACa                                                             <  1:1084970/100‑1 (MQ=255)
                                cAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCCGCGTTTTGTTATTCCACTGAAACAg                                                            >  2:1340210/1‑100 (MQ=255)
                                cAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAg                                                            <  1:768234/100‑1 (MQ=255)
                                  aCGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCa                                                          <  2:647258/100‑1 (MQ=255)
                                   ctgcggcATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCat                                                         <  1:1255650/98‑1 (MQ=255)
                                     gcggcATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCatat                                                       >  1:154518/1‑100 (MQ=255)
                                      cggcATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCata                                                        >  2:272577/1‑98 (MQ=255)
                                         catccatcCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGgc                                                   >  1:814220/1‑100 (MQ=255)
                                            ccatccaCCGGAGATGAAAACCCCGTCCACCGGTACACCCCGGCGCAAGGTGCCCCCGGCGCAGCCTCGTGTTCTGCCCCCGAAAAAGCatagcggt                                                   >  2:987360/1‑92 (MQ=255)
                                            ccatccaCCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCt                                                >  2:560986/1‑100 (MQ=255)
                                               tccaCCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGaa                                             <  2:587596/100‑1 (MQ=255)
                                                ccaCCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTACCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGaan                                            <  1:1376147/100‑2 (MQ=255)
                                                           gAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGc                                 >  2:802831/1‑100 (MQ=255)
                                                                cccAGTCCAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAg                            >  2:937156/1‑100 (MQ=255)
                                                                       cAACGGTACACCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGc                     >  1:117313/1‑100 (MQ=255)
                                                                              acacCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAg              >  2:1138998/1‑100 (MQ=255)
                                                                              acacCCCTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAg              <  1:495198/100‑1 (MQ=255)
                                                                                 ccccTGCGCCAGGTGCCACTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTAt           >  1:463556/1‑100 (MQ=255)
                                                                                  cccTGCGCCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTAtt          <  2:154518/100‑1 (MQ=255)
                                                                                   gcTGCGCCAGGGGCACCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTATTg         >  1:961033/2‑100 (MQ=255)
                                                                                      gcgcCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTATTgcgc      >  2:738660/1‑100 (MQ=255)
                                                                                        gcCAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTATTGCGCgg    <  1:606946/100‑1 (MQ=255)
                                                                                          cAGGTGCCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTATTGCGCGGcc  >  1:690356/1‑100 (MQ=255)
                                                                                               |                                                                                              
TCTGCATTCAGAAAAAATAAAATCTGGGATTTCAACGGCGGCATCCATCCACCGGAGATGAAAACCCAGTCCAACGGTACACCCCTGCGCCAGGTACCCCTGGCGCAGCGTTTTGTTATTCCACTGAAACAGCATATTGGCGCTGAAGGTGAGTTGTGCGTTAGCGTCGGCGATAAAGTATTGCGCGGCC  >  NC_000913/1706934‑1707123

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A