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 1,826,057 G→A 40.4% C89C (TGC→TGT)  hydN ← formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,826,0570GA40.4% 42.9 / 64.7 94C89C (TGC→TGT) hydNformate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
Reads supporting (aligned to +/- strand):  ref base G (8/48);  new base A (30/8);  total (38/56)
Fisher's exact test for biased strand distribution p-value = 3.04e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.70e-01

GGACGTACCACCACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCG  >  minE/1825995‑1826112
                                                              |                                                       
ggACGTACCACCACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGt                                                   <  1:2382082/69‑1 (MQ=255)
ggACGTACCACCACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGt                                                   <  1:632330/69‑1 (MQ=255)
ggACGTACCACCACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGt                                                   <  1:1977568/69‑1 (MQ=255)
    gcaccaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGG‑TTTGCAACCAATACAACGTTCCTg                                              <  1:1109903/67‑1 (MQ=255)
     caccaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:1839089/68‑1 (MQ=255)
     caccaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:1941835/68‑1 (MQ=255)
     caccaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:2751091/68‑1 (MQ=255)
     caccaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:3131434/68‑1 (MQ=255)
     caccaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:882258/68‑1 (MQ=255)
      accaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:1059809/68‑1 (MQ=255)
      accaccACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTg                                              <  1:3296520/68‑1 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCATGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:2559448/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTTCAtga                                         >  1:230923/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:2799605/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:2702831/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:190024/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:3274109/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:3289169/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:2365953/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:2543939/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:3360680/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:3360794/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:3382175/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:3386123/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1131313/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:898990/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1214330/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:889124/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:970680/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1375421/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1424302/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1443962/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:788914/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:633181/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1576877/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:450933/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1055175/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtga                                         >  1:1667714/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtg                                          >  1:1877275/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtg                                          >  1:134386/1‑67 (MQ=255)
          ccacTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATACAACGTTCCTGCAtg                                          >  1:1185998/1‑67 (MQ=255)
                   tCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACaa                                <  1:390899/69‑1 (MQ=255)
                     gCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAc                              <  1:2605121/69‑1 (MQ=255)
                     gCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAc                              <  1:299686/69‑1 (MQ=255)
                     gCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAc                              <  1:446504/69‑1 (MQ=255)
                     gCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAc                              <  1:975914/69‑1 (MQ=255)
                     gCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAc                              >  1:1065827/1‑69 (MQ=255)
                     gCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAc                              <  1:1721303/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:2778122/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:3246611/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:1817931/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:1757459/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:300272/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:2049547/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:16251/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:2117138/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:835651/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:2641200/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:2477304/69‑1 (MQ=255)
                       aCCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAAccc                            <  1:2527369/69‑1 (MQ=255)
                             cGGGCAAGCCACAACGCAGGTTTTGCAACCAATGc                                                        >  1:2554371/1‑35 (MQ=255)
                             cGGGCAAGCCACAACGCAGGTTTTGCAACCAATGc                                                        >  1:456629/1‑35 (MQ=255)
                             cGGGCAAGCCACAACGCAGGTTTTGCAACCAATGc                                                        >  1:1481610/1‑35 (MQ=255)
                             cGGGCAAGCCACAACGCAGGTTTTGCAACCAATGc                                                        >  1:1286755/1‑35 (MQ=255)
                             cGGGCAAGCCACAACGCAGGTTTTGCAACCAATGc                                                        >  1:3017850/1‑35 (MQ=255)
                             cGGGCAAGCCACAACGCAGGTTTTGCAACCAATGc                                                        >  1:2961787/1‑35 (MQ=255)
                               ggCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCAc                    <  1:3263127/69‑1 (MQ=255)
                               ggCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCAc                    <  1:1212950/69‑1 (MQ=255)
                               ggCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCAc                    <  1:1814438/69‑1 (MQ=255)
                               ggCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCAc                    <  1:2035715/69‑1 (MQ=255)
                               ggCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCAc                    <  1:2206176/69‑1 (MQ=255)
                               ggCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCAc                    <  1:2711276/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:1898404/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:905467/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:1861107/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:857251/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:1743820/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:2062045/69‑1 (MQ=255)
                                gCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:1567527/69‑1 (MQ=255)
                                   aGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:1060631/66‑1 (MQ=255)
                                   aGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCt                <  1:460535/69‑1 (MQ=255)
                                   aGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCt                <  1:1860925/69‑1 (MQ=255)
                                    gCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCt                <  1:3208499/68‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:1497202/69‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:1649673/69‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:79053/69‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:3172412/69‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:269936/69‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:3280406/69‑1 (MQ=255)
                                                 ttttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCg  <  1:921795/69‑1 (MQ=255)
                                                  tttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACg                   <  1:836063/51‑1 (MQ=255)
                                                  tttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGa              <  1:358941/56‑1 (MQ=255)
                                                  tttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGa              <  1:2284376/56‑1 (MQ=255)
                                                  tttGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTc   >  1:1253373/1‑67 (MQ=255)
                                                              |                                                       
GGACGTACCACCACTTCCATCGCACCATACGGGCAAGCCACAACGCAGGTTTTGCAACCAATGCAACGTTCCTGCATCACATGAACAAACCCTTTATCACGGCTGATAGCACCATTCG  >  minE/1825995‑1826112

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