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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,611,108 T→C 20.0% F185L (TTC→CTC)  hyfR → DNA‑binding transcriptional activator, formate sensing

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,611,1080TC20.0% 115.2 / 25.6 55F185L (TTC→CTC) hyfRDNA‑binding transcriptional activator, formate sensing
Reads supporting (aligned to +/- strand):  ref base T (35/9);  new base C (7/4);  total (42/13)
Fisher's exact test for biased strand distribution p-value = 4.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

ATGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGG  >  W3110S.gb/2611040‑2611173
                                                                    |                                                                 
aTGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCAtttttt                                                                  <  1:987657/70‑1 (MQ=255)
   cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGt                                                              >  1:1337538/1‑71 (MQ=255)
   cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGt                                                              >  1:2091509/1‑71 (MQ=255)
    aGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc                                                             >  1:2531537/1‑71 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                    >  1:3881936/1‑71 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                    >  1:3175206/1‑71 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACCTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                    >  1:2913659/1‑71 (MQ=255)
                tCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc                                                         >  1:3847707/1‑63 (MQ=255)
                tCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc                                                         >  1:2714646/1‑63 (MQ=255)
                tCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc                                                         >  1:1349860/1‑63 (MQ=255)
                tCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc                                                         >  1:1647225/1‑63 (MQ=255)
                  ttGATCTCTACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtcagtcag                                                >  1:2550814/1‑70 (MQ=255)
                  ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtcagtcag                                                >  1:2995935/1‑70 (MQ=255)
                  ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtcagtaag                                                >  1:2852814/1‑70 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTtctc                                                                 >  1:271255/1‑51 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGTCTTcagtcagt                                               <  1:3969112/69‑1 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTcagtcagt                                               <  1:2961327/69‑1 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATACATCATTTTTTCGGTCTGGCTTcagtcagt                                               <  1:622336/69‑1 (MQ=255)
                     aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtcagtcag                                                <  1:3508646/67‑1 (MQ=255)
                       ctcGACGATCTGATCGCTGACGTCGCTCGTTAGATCCATCATTTTTTCGGTc                                                             >  1:3040262/1‑52 (MQ=255)
                       ctcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCTGTc                                                             >  1:2319757/1‑52 (MQ=255)
                       ctcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc                                                             >  1:3617180/1‑52 (MQ=255)
                       ctcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc                                                             >  1:1470036/1‑52 (MQ=255)
                        tcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtc                                                       >  1:2781383/1‑56 (MQ=255)
                        tcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtc                                                  <  1:692676/62‑1 (MQ=255)
                        tcGACGATCTGATCGCTGACGTAGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa                                         >  1:36699/1‑71 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATgg                                           <  1:1358944/67‑1 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa                                         >  1:903565/1‑69 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACt                                       >  1:3581261/1‑71 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACt                                       >  1:3397646/1‑71 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACt                                       >  1:157938/1‑71 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGACTTCAGTCAGTATGGTACt                                       >  1:2003041/1‑71 (MQ=255)
                           acgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATgg                                           <  1:4084192/66‑1 (MQ=255)
                              aTCTGATCGCTGACGTCGCTCGTGAGATCCATCAttttt                                                                   <  1:730751/39‑1 (MQ=255)
                              aTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                       <  1:1226536/51‑1 (MQ=255)
                              aTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                       <  1:3909758/51‑1 (MQ=255)
                              aTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag                                                <  1:715147/58‑1 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTc                                                                 >  1:461648/1‑39 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTc                                                                 >  1:263302/1‑39 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTc                                                                 >  1:3652393/1‑39 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGa                                 >  1:938102/1‑71 (MQ=255)
                                   aTCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtcagt                                                   <  1:1109764/50‑1 (MQ=255)
                                             tCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAAc                    <  1:110549/71‑1 (MQ=255)
                                             tCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAAc                    <  1:2455869/71‑1 (MQ=255)
                                                          ccATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTAc                                        >  1:1249191/1‑38 (MQ=255)
                                                          ccATCATTTTTTCGGTCTGGCTTAAGTCAGTATGGTAc                                        >  1:2395452/1‑38 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGaa               >  1:3984046/1‑60 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGaa               >  1:1007387/1‑60 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGaa               >  1:1574333/1‑60 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgt    >  1:1332109/1‑71 (MQ=255)
                                                               attattTCGGTCTGGCTTCAGTCAGTATGGTACTCGGCGATCATCGAAAGaa                     >  1:2264385/1‑52 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgtg   >  1:382558/1‑70 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg  >  1:2531065/1‑71 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg  >  1:2539190/1‑71 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg  >  1:594659/1‑71 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg  >  1:2034941/1‑71 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg  >  1:1152182/1‑71 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTAAGTATGGTACTGGGCGa                                 >  1:1014456/1‑40 (MQ=255)
                                                               atTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg  >  1:3200117/1‑71 (MQ=255)
                                                                 tttttCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGt             <  1:3396825/58‑1 (MQ=255)
                                                                 tttttCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGt             <  1:2858094/58‑1 (MQ=255)
                                                                    |                                                                 
ATGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGG  >  W3110S.gb/2611040‑2611173

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