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 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,855,732 G→A 27.8% intergenic (‑270/‑17) ygbA ← / → mutS hypothetical protein/methyl‑directed mismatch repair protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,855,7320GA27.8% 84.5 / 37.0 54intergenic (‑270/‑17)ygbA/mutShypothetical protein/methyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base G (25/14);  new base A (9/6);  total (34/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.58e-01

CCGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT  >  W3110S.gb/2855664‑2855797
                                                                    |                                                                 
ccGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAggg                                                                   >  1:1103456/1‑69 (MQ=255)
ccGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAggg                                                                   >  1:2560453/1‑69 (MQ=255)
ccGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAggg                                                                   >  1:2568177/1‑69 (MQ=255)
     cgtctcgatctggtgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCg                                                              <  1:225489‑M2/18‑1 (MQ=255)
      gtctcgatctggtgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCg                                                              <  1:3703651‑M2/18‑1 (MQ=255)
        ctcgatctggtgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCGGa                                                            >  1:3634933‑M2/49‑68 (MQ=255)
        aTGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGa                                                            >  1:1406709/1‑68 (MQ=255)
        aTGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGa                                                            >  1:2962558/1‑68 (MQ=255)
         tcgatctggtgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCGGAc                                                           >  1:2421429‑M2/48‑68 (MQ=255)
         tcgatctggtgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCGGAc                                                           >  1:2400170‑M2/48‑68 (MQ=255)
              ctggtgcagaagaaaggcggaagttgcctatggcgagcataaTTTAATATCAGTAAACCGGACATAAcc                                                     >  1:2397875‑M2/43‑69 (MQ=255)
                 ttATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAAcccc                                                   >  1:3694439/1‑68 (MQ=255)
                 ttATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACAGGACATAACCC                                                    >  1:3698551‑M1/1‑67 (MQ=255)
                  tgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCGGACATAaccca                                                   >  1:1287086‑M2/39‑66 (MQ=255)
                  tgcagaagaaaggcggaagttgcctctggcgagcataaTTTAATATCAGTAAACCGGACATAaccca                                                   >  1:2977166‑M2/39‑66 (MQ=255)
                     gtgATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATg                                                <  1:698119/67‑1 (MQ=255)
                           aCAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATg                                                >  1:1087535/1‑61 (MQ=255)
                            cAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAAt                                        >  1:3244395/1‑68 (MQ=255)
                             aaCGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATa                                       >  1:2039303/1‑68 (MQ=255)
                                ggaagttgcctctggcgagcataaTTTAATATCAGTAAACCGGACATAAc                                                      >  1:377743‑M2/25‑50 (MQ=255)
                                     tAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              <  1:896511/69‑1 (MQ=255)
                                     tAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              <  1:104425/69‑1 (MQ=255)
                                     tAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              <  1:201149/69‑1 (MQ=255)
                                       aaaaCCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCg                             >  1:2480458/1‑68 (MQ=255)
                                           ccATCACACCCCATTTAATATCCGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcc                        <  1:1247392/69‑1 (MQ=255)
                                           ccATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcc                        <  1:1566273/69‑1 (MQ=255)
                                             aTCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgccca                      <  1:2033477/69‑1 (MQ=255)
                                                acacCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCTATAGAAAATTTCGacgcccatac                   >  1:405432/1‑69 (MQ=255)
                                                   ccccATTTAATATCAGGGAACCGGACATAACCCCATGAGTGc                                           <  1:3657685/42‑1 (MQ=255)
                                                   ccccATTTAATATCAGGGAACCGGACATAACCCCATGAGTGc                                           >  1:1415752/1‑42 (MQ=255)
                                                     taattTAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcagggg               >  1:430618‑M1/3‑31 (MQ=255)
                                                     taattTAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcagggg               >  1:3471435‑M1/3‑31 (MQ=255)
                                                      cATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatacgcccat             <  1:714819/69‑1 (MQ=255)
                                                       aTTTAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcagggggca            <  1:2134477‑M1/69‑41 (MQ=255)
                                                       aTTTAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtggg                     <  1:808827‑M1/60‑32 (MQ=255)
                                                        tttAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgccca                      <  1:1812554/58‑1 (MQ=255)
                                                        tttAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCatga           <  1:1546564/69‑1 (MQ=255)
                                                          tAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttt                                <  1:968154‑M1/46‑21 (MQ=255)
                                                          tAATATCAGGGTACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCatg            >  1:3655943/1‑66 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGaa                                    <  1:863232/42‑1 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatacgcccat             >  1:1112779/1‑65 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgccca                      >  1:781559/1‑56 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGa                            >  1:335435/1‑50 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCatga           >  1:3428636/1‑67 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCatga           >  1:1887159/1‑67 (MQ=255)
                                                          tAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCatga           >  1:632388/1‑67 (MQ=255)
                                                            atatCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcagggggcaagta        <  1:1162505‑M1/68‑45 (MQ=255)
                                                              atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatacgcccat             <  1:710420/61‑1 (MQ=255)
                                                               tCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgccca                      >  1:2818938/1‑51 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAAt                                 >  1:2053528/1‑39 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              >  1:565382/1‑42 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              >  1:3554414/1‑42 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              >  1:3686725/1‑42 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                              >  1:2217035/1‑42 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATgc        >  1:3068451/1‑64 (MQ=255)
                                                                cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATgc        >  1:240222/1‑64 (MQ=255)
                                                                 aGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGt  <  1:2126622/69‑1 (MQ=255)
                                                                    gAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgc                         <  1:3125590/43‑1 (MQ=255)
                                                                    gAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgc                         <  1:3404432/43‑1 (MQ=255)
                                                                    |                                                                 
CCGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT  >  W3110S.gb/2855664‑2855797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A