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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,220,648 C→T 25.0% P527S (CCA→TCA)  aceB → malate synthase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,220,6480CT25.0% 103.9 / 34.1 56P527S (CCA→TCA) aceBmalate synthase A
Reads supporting (aligned to +/- strand):  ref base C (16/26);  new base T (8/6);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 2.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

TTGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCG  >  W3110S.gb/4220580‑4220711
                                                                    |                                                               
ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                 >  1:2774144/1‑69 (MQ=255)
ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                 >  1:3300297/1‑69 (MQ=255)
ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                 >  1:2426190/1‑69 (MQ=255)
ttGACGATGCCGCACGCTTGATGGAAAAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                 >  1:1894208/1‑69 (MQ=255)
  gACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAgg                                                             >  1:220605/1‑71 (MQ=255)
     gATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTa                                                          <  1:2891583/71‑1 (MQ=255)
         ccGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGc                                                      <  1:292571/71‑1 (MQ=255)
          cGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGcc                                                     >  1:4620247/1‑71 (MQ=255)
             aCGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGt                                                  <  1:3151268/71‑1 (MQ=255)
               gCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTa                                                <  1:3058315/71‑1 (MQ=255)
                cTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTAc                                                         >  1:4075434/1‑61 (MQ=255)
                  tGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCg                                             >  1:2278474/1‑71 (MQ=255)
                  tGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCg                                             >  1:932749/1‑71 (MQ=255)
                  tGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCg                                             >  1:2365956/1‑71 (MQ=255)
                   gATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCg                                             >  1:2479048/1‑70 (MQ=255)
                   gATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCg                                             <  1:2963711/70‑1 (MQ=255)
                    aTGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTa                                           <  1:2969258/71‑1 (MQ=255)
                        aaCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAacc                                       <  1:2469171/71‑1 (MQ=255)
                         aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAacca                                      <  1:668586/71‑1 (MQ=255)
                         aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaa                                          <  1:2397839/67‑1 (MQ=255)
                         aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaa                                          <  1:4012222/67‑1 (MQ=255)
                         aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaa                                          <  1:1079337/67‑1 (MQ=255)
                          cAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAaccac                                     <  1:3098228/71‑1 (MQ=255)
                          cAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                     >  1:4342932/1‑71 (MQ=255)
                             aTCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                  <  1:4224610/55‑1 (MQ=255)
                              tCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACcaca                                 >  1:2996741/1‑71 (MQ=255)
                                accacTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACAt                                >  1:4734642/1‑70 (MQ=255)
                                 ccacTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCt                                                    <  1:3582470/49‑1 (MQ=255)
                                  cacTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAAc                             <  1:2359679/71‑1 (MQ=255)
                                  cacTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAAc                             <  1:1104619/71‑1 (MQ=255)
                                   acTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAAc                             >  1:4464904/1‑70 (MQ=255)
                                   acTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACt                            <  1:1016423/71‑1 (MQ=255)
                                       ccGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTa                                           >  1:4330917/1‑52 (MQ=255)
                                       ccGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTa                                           >  1:13279/1‑52 (MQ=255)
                                        cGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATgg                        <  1:4271181/70‑1 (MQ=255)
                                               ttAATTGATTTCCTGACCTTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTg                >  1:1599440/1‑71 (MQ=255)
                                               ttAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTg                >  1:5056616/1‑71 (MQ=255)
                                               ttAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                     <  1:3841604/66‑1 (MQ=255)
                                               ttAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                     <  1:914068/66‑1 (MQ=255)
                                               ttAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATc                  <  1:4551590/69‑1 (MQ=255)
                                                 aaTTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca              >  1:2990679/1‑71 (MQ=255)
                                                 aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca              >  1:2954229/1‑71 (MQ=255)
                                                 aaTTGATTTCCTGACACTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCt                 >  1:3033032/1‑68 (MQ=255)
                                                  aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac             <  1:2717350/71‑1 (MQ=255)
                                                  aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac             <  1:2723339/71‑1 (MQ=255)
                                                  aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca              <  1:341041/70‑1 (MQ=255)
                                                   ttGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcaca            >  1:2482785/1‑71 (MQ=255)
                                                   ttGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac             <  1:971566/70‑1 (MQ=255)
                                                     gATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACAt           >  1:5090131/1‑70 (MQ=255)
                                                     gATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACAt           >  1:4226948/1‑70 (MQ=255)
                                                       tttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                           <  1:4533946/52‑1 (MQ=255)
                                                       tttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                           <  1:4694240/52‑1 (MQ=255)
                                                       tttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                           <  1:939596/52‑1 (MQ=255)
                                                       tttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaa        <  1:4869641/71‑1 (MQ=255)
                                                        ttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaa        >  1:3111821/1‑70 (MQ=255)
                                                         tCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaaa      >  1:2701205/1‑71 (MQ=255)
                                                              aCCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg  >  1:1859322/1‑70 (MQ=255)
                                                              aCCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg  <  1:1073085/70‑1 (MQ=255)
                                                                  tGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaaa      <  1:3151634/62‑1 (MQ=255)
                                                                  tGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaaa      <  1:1549353/62‑1 (MQ=255)
                                                                    ccAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAcc    >  1:2059163/1‑62 (MQ=255)
                                                                    |                                                               
TTGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCG  >  W3110S.gb/4220580‑4220711

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A