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 2,883,780 G→C 44.4% A276A (GCC→GCG)  cpdB ← 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,883,7800GC44.4% 25.6 / 108.2 98A276A (GCC→GCG) cpdB2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base G (29/25);  new base C (18/25);  total (47/51)
Fisher's exact test for biased strand distribution p-value = 3.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.50e-01

TCGACCACACCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCAAA  >  minE/2883712‑2883845
                                                                    |                                                                 
tCGACCACACCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTg                                                                   >  1:1242986/1‑69 (MQ=255)
  gACCACACCAAGATGATCGCCCCACATGCCTGGCATTACCGC‑‑‑AACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:769936/69‑1 (MQ=255)
    ccACACCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGa                                                               <  1:517115/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCATCGTGCCTTTCGCGat                                                              <  1:1463334/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:3054027/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2133602/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2206601/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1995557/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:220970/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2435849/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:254889/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1854163/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1784738/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2825195/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2831777/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1632918/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:324418/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1080357/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:859920/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:3393535/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:401376/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:822316/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1181907/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:1375657/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:558372/69‑1 (MQ=255)
     cacaCCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTAGCGat                                                              <  1:1654543/69‑1 (MQ=255)
      acacCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2660721/68‑1 (MQ=255)
           aaGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGc                                                        >  1:997127/1‑69 (MQ=255)
              atgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGcccc                                                     >  1:3323515/1‑69 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGcccc                                                     >  1:2670282/1‑68 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGccc                                                      >  1:1733074/1‑67 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCt                                                    >  1:258671/1‑69 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCt                                                    >  1:2607113/1‑69 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCt                                                    >  1:2908358/1‑69 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCt                                                    >  1:882010/1‑69 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCt                                                    >  1:1070120/1‑69 (MQ=255)
               tgatCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCt                                                    >  1:1055227/1‑69 (MQ=255)
                   cGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGa                                                <  1:349433/69‑1 (MQ=255)
                   cGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTCGCGat                                                              <  1:2439703/55‑1 (MQ=255)
                                       aCCGCCGGAACCCCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:558596/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTAcc                             >  1:1804620/1‑68 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:1137798/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:859409/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:134980/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:2046911/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:291546/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:1718287/1‑69 (MQ=255)
                                       aCCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCt                            >  1:2537694/1‑69 (MQ=255)
                                            cgGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGaa                       <  1:1651613/69‑1 (MQ=255)
                                            cgGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGaa                       <  1:532302/69‑1 (MQ=255)
                                            cgGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGaa                       <  1:446160/69‑1 (MQ=255)
                                            cgGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGaa                       <  1:1606029/69‑1 (MQ=255)
                                             gtaaCACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGaa                       <  1:2576179/66‑1 (MQ=255)
                                               aaCACCATTCAGCGTGCCTTTCGCGATATCAGCCCCTTCGATATCAGCa                                        >  1:2191282/1‑49 (MQ=255)
                                               aaCACCATTCAGCGTGCCTTTCGCGATATCAGCCCCTTCGATATCAGCa                                        >  1:1634485/1‑49 (MQ=255)
                                                   ccATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACgg                  >  1:605340/1‑67 (MQ=255)
                                                   ccATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGc                 >  1:1586087/1‑68 (MQ=255)
                                                   ccATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGc                 >  1:534239/1‑68 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2093/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2235484/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:43522/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2138689/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:3057327/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2942451/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2280244/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2855504/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:168473/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2822894/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:1157703/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2381717/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2057378/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:2418405/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:1840824/1‑35 (MQ=255)
                                                   ccATTCAGCGTGCCTTTCGCGATATCAGCCCCTTc                                                  >  1:1126062/1‑35 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1175786/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:729301/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:2136548/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1985105/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:880382/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1371729/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:512133/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:3290384/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1683710/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:2425632/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1776425/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:2761597/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1477548/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:2973439/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:1982811/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:224232/69‑1 (MQ=255)
                                                       tCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACAGCGTGAg            <  1:850029/69‑1 (MQ=255)
                                                            gTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAg            <  1:2062023/64‑1 (MQ=255)
                                                               ccTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCa    >  1:865430/1‑69 (MQ=255)
                                                               ccTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCa    >  1:2564200/1‑69 (MQ=255)
                                                               ccTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCa    >  1:1946432/1‑69 (MQ=255)
                                                                  ttGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCaaa  >  1:1607892/1‑68 (MQ=255)
                                                                  ttGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCaaa  >  1:2725568/1‑68 (MQ=255)
                                                                  ttGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCaaa  >  1:224211/1‑68 (MQ=255)
                                                                  ttGGCGATATAAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGa                        >  1:3138071/1‑46 (MQ=255)
                                                                    |                                                                 
TCGACCACACCAAGATGATCGCCCCACATGCCTGGCATTACCGCCGGAACACCATTCAGCGTGCCTTTGGCGATATCAGCCCCTTCGATATCAGCAAAATCTTTACCTGGGAAAACGGCGTGAGCATGGCCAAA  >  minE/2883712‑2883845

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