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 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,220,648 C→T 15.6% P527S (CCA→TCA)  aceB → malate synthase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,220,6480CT15.6% 200.9 / 25.5 77P527S (CCA→TCA) aceBmalate synthase A
Reads supporting (aligned to +/- strand):  ref base C (38/27);  new base T (10/2);  total (48/29)
Fisher's exact test for biased strand distribution p-value = 1.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-01

TTTTGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTACAC  >  W3110S.gb/4220578‑4220716
                                                                      |                                                                    
ttttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      <  1:1904572/71‑1 (MQ=255)
  ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      >  1:1944823/1‑69 (MQ=255)
  ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      >  1:320019/1‑69 (MQ=255)
   tGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAg                                                                   >  1:1705767/1‑71 (MQ=255)
      cGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGc                                                                 >  1:1211667/1‑70 (MQ=255)
      cGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCt                                                                <  1:3189454/71‑1 (MQ=255)
        aTGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      <  1:2728529/63‑1 (MQ=255)
            cGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGcc                                                          <  1:4301289/71‑1 (MQ=255)
            cGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGcc                                                          <  1:505184/71‑1 (MQ=255)
             gCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCt                                                         >  1:3504348/1‑71 (MQ=255)
              cACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCt                                                         >  1:1832161/1‑70 (MQ=255)
               aCGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                       >  1:1200837/1‑71 (MQ=255)
               aCGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                       >  1:1353321/1‑71 (MQ=255)
                cGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTACTGACCCTGCCAGGCTACCGCCTGt                                                       >  1:1258804/1‑70 (MQ=255)
                 gCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      >  1:1975911/1‑54 (MQ=255)
                 gCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGc                                                                 <  1:2313288/59‑1 (MQ=255)
                  cTTGATGGAACAGATCACCACTTCCGATTAGTTAATTGATTTCCTGACCCTGCCAGGc                                                                 <  1:4025586/58‑1 (MQ=255)
                    tGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCg                                                  >  1:150114/1‑71 (MQ=255)
                     gATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGc                                                   >  1:4320286/1‑69 (MQ=255)
                     gATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTACTGACCCTGTCAGGCTACCGCCTGTTAGCg                                                  >  1:3526784/1‑70 (MQ=255)
                      attgAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGt                                                 >  1:3388613/4‑70 (MQ=255)
                      aTGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAg                                                                   >  1:1576999/1‑52 (MQ=255)
                      aTGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGt                                                 <  1:1725876/70‑1 (MQ=255)
                       tGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCa                                                                    >  1:1043981/1‑50 (MQ=255)
                       tGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaa                                               <  1:2906306/71‑1 (MQ=255)
                         gAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAac                                             >  1:4194312/1‑71 (MQ=255)
                         gAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAgg                                                                  >  1:3561257/1‑50 (MQ=255)
                         gAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAac                                             <  1:3096250/71‑1 (MQ=255)
                           aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaaa                                              >  1:2495456/1‑68 (MQ=255)
                           aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAacca                                           <  1:2149688/71‑1 (MQ=255)
                           aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAacca                                           <  1:2905029/71‑1 (MQ=255)
                            cAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                          >  1:3952468/1‑71 (MQ=255)
                            cAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                          <  1:3141140/71‑1 (MQ=255)
                              gATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                          <  1:186578/69‑1 (MQ=255)
                               aTCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGc                                                   <  1:3936013/59‑1 (MQ=255)
                                tCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTa                                                     >  1:52326/1‑56 (MQ=255)
                                 caccacTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTATacca                                           <  1:3381782/65‑1 (MQ=255)
                                 caccacTTCCGATGAGTTAATTGATTTCCTGACACTGCCAGGCTACCGCCTGTTAGCGTAAACCACcaca                                      >  1:4459335/1‑70 (MQ=255)
                                   ccacTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTa                                                     >  1:1764156/1‑53 (MQ=255)
                                      cTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGt                                                       >  1:2894549/1‑48 (MQ=255)
                                      cTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                                >  1:2907977/1‑71 (MQ=255)
                                      cTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                                >  1:3868413/1‑71 (MQ=255)
                                      cTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                                >  1:3735173/1‑71 (MQ=255)
                                        tCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:1362536/1‑71 (MQ=255)
                                        tCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:3825789/1‑71 (MQ=255)
                                        tCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:1814876/1‑71 (MQ=255)
                                         ccGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaaa                                              >  1:4470286/1‑54 (MQ=255)
                                         ccGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:249874/1‑70 (MQ=255)
                                          cGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                       <  1:1271756/44‑1 (MQ=255)
                                            aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaaa                                              >  1:4448344/1‑51 (MQ=255)
                                            aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACcaccac                                       <  1:2979164/58‑1 (MQ=255)
                                            aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAg                           >  1:4494293/1‑70 (MQ=255)
                                            aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                          <  1:2559733/71‑1 (MQ=255)
                                            aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                          <  1:2832510/71‑1 (MQ=255)
                                             tGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccacc                                         >  1:3189091/1‑55 (MQ=255)
                                               aGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATc                       <  1:458711/71‑1 (MQ=255)
                                                   aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGtt                                                      >  1:2383275/1‑36 (MQ=255)
                                                   aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccacc                                         <  1:705565/49‑1 (MQ=255)
                                                   aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCt                      >  1:1055971/1‑68 (MQ=255)
                                                   aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca                   >  1:2043951/1‑71 (MQ=255)
                                                   aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca                   >  1:813210/1‑71 (MQ=255)
                                                    aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                          <  1:3972692/63‑1 (MQ=255)
                                                    aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac                  <  1:3126994/71‑1 (MQ=255)
                                                    aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac                  <  1:8086/71‑1 (MQ=255)
                                                     ttGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcaca                 <  1:3995554/71‑1 (MQ=255)
                                                     ttGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcaca                 <  1:726640/71‑1 (MQ=255)
                                                       gATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACAt                <  1:4382331/70‑1 (MQ=255)
                                                         tttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaa             <  1:771533/71‑1 (MQ=255)
                                                          ttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaa             >  1:4560080/1‑70 (MQ=255)
                                                           tCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaaa           >  1:3004650/1‑71 (MQ=255)
                                                           tCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaa            <  1:4514281/70‑1 (MQ=255)
                                                             cTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACAt                                     >  1:1331077/1‑43 (MQ=255)
                                                              tGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAg                           >  1:227136/1‑52 (MQ=255)
                                                              tGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAccc        >  1:4387624/1‑71 (MQ=255)
                                                              tGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAccc        >  1:1419274/1‑71 (MQ=255)
                                                               gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACAt                                     <  1:1561703/41‑1 (MQ=255)
                                                               gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAccc        >  1:3442563/1‑70 (MQ=255)
                                                               gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg       >  1:1012138/1‑71 (MQ=255)
                                                               gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg       >  1:1838985/1‑71 (MQ=255)
                                                               gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg       >  1:851421/1‑71 (MQ=255)
                                                                     gCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTacac  >  1:2224912/1‑70 (MQ=255)
                                                                     gCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTacac  >  1:2003864/1‑70 (MQ=255)
                                                                      ccAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTacac  <  1:3842384/69‑1 (MQ=255)
                                                                      |                                                                    
TTTTGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTACAC  >  W3110S.gb/4220578‑4220716

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