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 F1 I0 R2 532 47.8 3863072 94.9% 3666055 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,717,255 A→T 23.5% intergenic (‑71/‑136) yfiF ← / → trxC predicted methyltransferase/thioredoxin 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,717,2550AT23.5% 60.8 / 16.3 34intergenic (‑71/‑136)yfiF/trxCpredicted methyltransferase/thioredoxin 2
Reads supporting (aligned to +/- strand):  ref base A (18/8);  new base T (2/6);  total (20/14)
Fisher's exact test for biased strand distribution p-value = 4.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAGCGCGCAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTCCCCGATAATAT  >  W3110S.gb/2717208‑2717325
                                               |                                                                      
gAAGCGCGCAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATAcc                                                 >  1:725693/1‑71 (MQ=255)
gAAGCGCGCAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATAcc                                                 >  1:588916/1‑71 (MQ=255)
    cgcgcAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCt                                                               >  1:2230338/1‑53 (MQ=255)
      cgcAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTTCCAAAGCCTGTGTCTATCATACCCATTg                                            >  1:176619/1‑70 (MQ=255)
      cgcAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTTCCAAAGCCTGTGTCTATCATACCCATTg                                            >  1:2970235/1‑70 (MQ=255)
       gcAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGaa                                          >  1:3313621/1‑71 (MQ=255)
          gATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATaa                                       <  1:3417639/71‑1 (MQ=255)
           aTTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTAt                                                       <  1:1165964/54‑1 (MQ=255)
           aTTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTAt                                                       <  1:3556051/54‑1 (MQ=255)
            ttACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATaaaa                                     >  1:2183619/1‑71 (MQ=255)
              aCCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATaaaa                                     >  1:497999/1‑69 (MQ=255)
              aCCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATaaaa                                     >  1:425331/1‑69 (MQ=255)
               cccGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGc                                                             <  1:1525219/44‑1 (MQ=255)
               cccGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGc                                                             <  1:3714421/44‑1 (MQ=255)
                        cgcgcgGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTc                         >  1:3353248/1‑71 (MQ=255)
                         gcgcgGTTCGCCATGATTTCGTTCCAAAGCCTGTGTCTATCATACCCATTGAATAAAAc                                    <  1:631071/59‑1 (MQ=255)
                         gcgcgGTTCGCCATGATTTCGTTCCAAAGCCTGTGTCTATCATACCCATTGAATAAAAc                                    <  1:2244639/59‑1 (MQ=255)
                            cgGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATtgttgt                          >  1:1597035/1‑66 (MQ=255)
                             ggTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGaa                    <  1:2019507/71‑1 (MQ=255)
                               ttCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACa                  <  1:439341/71‑1 (MQ=255)
                                     aTGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGaa                                          >  1:3532970/1‑41 (MQ=255)
                                     aTGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACa                                   >  1:97114/1‑48 (MQ=255)
                                     aTGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACa                                   >  1:1533706/1‑48 (MQ=255)
                                     aTGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTcc            >  1:2273076/1‑71 (MQ=255)
                                     aTGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTcc            >  1:588687/1‑71 (MQ=255)
                                       gATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTccac          >  1:1914775/1‑69 (MQ=255)
                                        aTTTCGTTCCAAAGCCTGTGTCTATCATACCCATTGAATAAAACAGAttg                              <  1:2056600/50‑1 (MQ=255)
                                        aTTTCGTTCCAAAGCCTGTGTCTATCATACCCATTGAATAAAACAGAttg                              <  1:2504746/50‑1 (MQ=255)
                                        aTTTCGTTCCAAAGCCTGTGTCTATCATACCCATTGAATAAAACAGAttg                              <  1:615168/50‑1 (MQ=255)
                                        aTTTCGTTCCAAAGCCTGTGTCTATCATACCCATTGAATAAAACAGAttg                              <  1:2868099/50‑1 (MQ=255)
                                        aTTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTcccc          >  1:2567764/1‑70 (MQ=255)
                                        aTTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTcccc          >  1:2878066/1‑70 (MQ=255)
                                         tttCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTCCCCGa        >  1:3374073/1‑71 (MQ=255)
                                            cGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTCCCCGata      <  1:478021/70‑1 (MQ=255)
                                               aCCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTCCCCGATAatat  >  1:431207/1‑71 (MQ=255)
                                               |                                                                      
GAAGCGCGCAGATTACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTACCAAAGCCTGCGACTATCATACCTATTGAATAAAACAGATTGTTGTCTGGAACAATGTCCCCGATAATAT  >  W3110S.gb/2717208‑2717325

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A