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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 468,888 C→T 26.1% V304V (GTC→GTT)  sucB → dihydrolipoyltranssuccinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE468,8880CT26.1% 147.9 / 46.1 122V304V (GTC→GTT) sucBdihydrolipoyltranssuccinase
Reads supporting (aligned to +/- strand):  ref base C (49/41);  new base T (11/21);  total (60/62)
Fisher's exact test for biased strand distribution p-value = 6.45e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.03e-01

Only 100 of 140 total aligned reads displayed.

TGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGG  >  minE/468834‑468956
                                                      |                                                                    
tGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:1000384/1‑68 (MQ=255)
tGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:2465004/1‑68 (MQ=255)
tGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:3002209/1‑68 (MQ=255)
tGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:214759/1‑68 (MQ=255)
tGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:2680755/1‑68 (MQ=255)
tGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:691850/1‑68 (MQ=255)
tGTCAATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCTGTTAAAGGCCGTGACg                                                         >  1:1808233/1‑68 (MQ=255)
  tCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGc                                                       >  1:907060/1‑68 (MQ=255)
       aCCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTg                                                 >  1:3235860/1‑69 (MQ=255)
       aCCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTg                                                 >  1:2433913/1‑69 (MQ=255)
       aCCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTg                                                 >  1:2385584/1‑69 (MQ=255)
       aCCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTg                                                 >  1:959400/1‑69 (MQ=255)
          cTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGt                                                             >  1:2812673/1‑54 (MQ=255)
          cTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:2034396/1‑69 (MQ=255)
            cGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGt                                            <  1:263998/69‑1 (MQ=255)
            cGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGt                                            <  1:3409189/69‑1 (MQ=255)
            cGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGt                                            <  1:312063/69‑1 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:7170/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:2719872/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:2360415/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:1960190/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:410009/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:1873606/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAcc                                              >  1:351953/1‑63 (MQ=255)
                aTGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGCCCGTGACGGCAAGCTGAc                                               >  1:1781561/1‑62 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTTACGGCa                                                      >  1:2854849/1‑52 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2447632/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2772115/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      >  1:2882963/1‑52 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      >  1:282122/1‑52 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2696252/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      >  1:2373117/1‑52 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      >  1:2724672/1‑52 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2334865/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2201701/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2197469/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2029454/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:3380813/52‑1 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      >  1:619069/1‑52 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGa                                      >  1:1153880/1‑68 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGAt                                     >  1:601214/1‑69 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGAt                                     >  1:731965/1‑69 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGAt                                     >  1:2686793/1‑69 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGAt                                     >  1:943191/1‑69 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGAt                                     >  1:3335682/1‑69 (MQ=255)
                   gCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTCACGGCa                                                      <  1:1272039/52‑1 (MQ=255)
                    cAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCa                                                      <  1:2643778/51‑1 (MQ=255)
                     aGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCa                                                                     <  1:1824293/35‑1 (MQ=255)
                     aGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCa                                                                     <  1:3099029/35‑1 (MQ=255)
                     aGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCa                                                                     <  1:1095056/35‑1 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGAGCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:192661/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACtt                    >  1:3050523/1‑67 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:2243755/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:1471688/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:1510229/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:2870345/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:1727959/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:2441474/1‑68 (MQ=255)
                                      tCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   >  1:2251091/1‑68 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAATATCTGACCGGTGGTAACTtcacc                <  1:706358/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:845816/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:1034059/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:2577654/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:2555404/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:194396/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:2407891/69‑1 (MQ=255)
                                        aaaGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcacc                <  1:1245343/69‑1 (MQ=255)
                                          agagCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGt                                            <  1:1739757/39‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAATCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:1856544/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:2769601/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:2539807/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:2525069/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:414539/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:103853/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:1859582/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:2336190/69‑1 (MQ=255)
                                              cTGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:3404601/69‑1 (MQ=255)
                                               tGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:593063/68‑1 (MQ=255)
                                               tGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:1965936/68‑1 (MQ=255)
                                               tGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:1546993/68‑1 (MQ=255)
                                               tGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:1351823/68‑1 (MQ=255)
                                               tGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:2422217/68‑1 (MQ=255)
                                               tGGCTGTTAAAGGCCGTGACGGCAAGCTGACGGTTGAAGATCTGACCGGTGGTAACTtcaccatcacc          <  1:291885/68‑1 (MQ=255)
                                                 gCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcaccat              <  1:833679/62‑1 (MQ=255)
                                                 gCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcaccat              <  1:1245295/62‑1 (MQ=255)
                                                 gCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcaccat              <  1:2740626/62‑1 (MQ=255)
                                                 gCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcaccat              <  1:3360326/62‑1 (MQ=255)
                                                 gCAGGCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtcaccat              <  1:537265/62‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   <  1:196037/52‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   <  1:1638593/52‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   <  1:1355750/52‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   <  1:74645/52‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   <  1:3220628/52‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTtc                   <  1:2437742/52‑1 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACggtgg  >  1:1455461/1‑69 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACggtgg  >  1:3302796/1‑69 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACggtgg  >  1:2374726/1‑69 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACggtgg  >  1:2519356/1‑69 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACggtg   >  1:550432/1‑68 (MQ=255)
                                                      cAAAGGCCGTGACGGCAAGCTGACAGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACggtgg  >  1:3407585/1‑69 (MQ=255)
                                                      |                                                                    
TGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGG  >  minE/468834‑468956

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