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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 1,657,562 T→C I14T (ATT→ACT)  ynfB → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,657,5620TC84.0% 258.0 / 36.9 100I14T (ATT→ACT) ynfBhypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (13/3);  new base C (45/39);  total (58/42)
Fisher's exact test for biased strand distribution p-value = 5.31e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

CAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATT  >  W3110S.gb/1657509‑1657626
                                                     |                                                                
cAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTgcg                                                    >  1:2309854/1‑68 (MQ=255)
cAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTgcg                                                    >  1:45661/1‑68 (MQ=255)
cAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTgcg                                                    >  1:4052430/1‑68 (MQ=255)
   ggAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTgg                                              <  1:36670/71‑1 (MQ=255)
    gaatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTgg                                              <  1:2568478/70‑1 (MQ=255)
     aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCa                                            <  1:809212/71‑1 (MQ=255)
     aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCa                                            <  1:3403862/71‑1 (MQ=255)
     aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCa                                            <  1:1583779/71‑1 (MQ=255)
     aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCa                                            <  1:2652424/71‑1 (MQ=255)
           ttATGAAATTCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:1048791/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTctg                                                              >  1:2320471/1‑47 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGa                                        >  1:969803/1‑69 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:353217/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:975164/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:3468378/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:19849/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:217861/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:2590400/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:2448476/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:1731826/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:91446/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:1276089/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:1639704/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:3786256/1‑70 (MQ=255)
           ttATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:3863736/1‑70 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:1798202/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:2463316/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:2582524/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:709684/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:2589324/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:519629/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:2642629/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:2677700/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:3169432/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:3689644/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:1676543/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:364878/1‑71 (MQ=255)
            tATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:3566933/1‑71 (MQ=255)
            tATGAAAATCACTCTAAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGca                                     >  1:1676993/1‑71 (MQ=255)
                  aaTCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAAc                                 >  1:2644669/1‑69 (MQ=255)
                  aaTCACTCTCAGCAAACGAATCGGCCTGCTAGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       >  1:632910/1‑63 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:4091706/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:4034242/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:2380306/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:1651807/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:1831472/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:2152198/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:1921202/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:3216750/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                       <  1:2903793/61‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                             <  1:1823048/71‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                             <  1:112775/71‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                             <  1:1450394/71‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                             <  1:3546738/71‑1 (MQ=255)
                    tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                             <  1:2131758/71‑1 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgcgc                                                   >  1:2979758/1‑48 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgcg                                                    >  1:2892225/1‑47 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:2765096/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:1405623/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:1354891/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:131795/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:2444527/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:2246537/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:3752637/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:3420968/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:3526428/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTATTATGCTGCCTTGCGCa                                                  >  1:1668658/1‑49 (MQ=255)
                     cACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                             <  1:2436217/70‑1 (MQ=255)
                     cACTCTAAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCa                                                  >  1:3397903/1‑49 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:3790969/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:58102/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:3848236/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:4002864/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:676168/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:840910/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:1912053/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:2139319/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:3387026/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:1218022/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:1212776/71‑1 (MQ=255)
                            aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:2983848/71‑1 (MQ=255)
                             gCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                     <  1:2449797/70‑1 (MQ=255)
                               aaaCGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAAc                  <  1:2098360/71‑1 (MQ=255)
                               aaaCGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAAc                  <  1:317449/71‑1 (MQ=255)
                               aaaCGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAAc                  <  1:1313473/71‑1 (MQ=255)
                               aaaCGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAAc                  <  1:1346455/71‑1 (MQ=255)
                               aaaCGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAAc                  <  1:1709643/71‑1 (MQ=255)
                                    aaTCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa             <  1:3801148/71‑1 (MQ=255)
                                    aaTCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa             <  1:805941/71‑1 (MQ=255)
                                    aaTCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa             <  1:3949980/71‑1 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:2267060/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:2915627/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:218461/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:739997/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:1523466/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:2313375/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:454969/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:3908352/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt  >  1:2557845/1‑70 (MQ=255)
                                                cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAt   >  1:2485080/1‑69 (MQ=255)
                                                     |                                                                
CAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATT  >  W3110S.gb/1657509‑1657626

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