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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 608,370 C→T 15.8% A628A (GCG→GCA) ‡ pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE608,3700CT15.8% 136.9 / 16.3 57A628A (GCG→GCA) ‡pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base C (26/22);  new base T (4/5);  total (30/27)
Fisher's exact test for biased strand distribution p-value = 7.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

CGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGT  >  minE/608300‑608438
                                                                      |                                                                    
cGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGgc                                                                      >  1:1922/1‑71 (MQ=255)
 ggAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGgcg                                                                     >  1:3165444/1‑71 (MQ=255)
    aGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGgcgcgc                                                                  >  1:779293/1‑71 (MQ=255)
        agagagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCa                                                                <  1:1961746/69‑1 (MQ=255)
        agagagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGc                                                              <  1:2220336/71‑1 (MQ=255)
          agagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                                                            <  1:2923959/71‑1 (MQ=255)
           gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                                                            >  1:1172352/1‑70 (MQ=255)
           gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                                                            >  1:696155/1‑70 (MQ=255)
             ggCTACTGCACCTTTCTGGACACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCacgac                                                         <  1:3200847/71‑1 (MQ=255)
              gCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                                                            <  1:836964/67‑1 (MQ=255)
                tACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACgacgac                                                      >  1:3728350/1‑71 (MQ=255)
                    gCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCacga                                                          >  1:2314731/1‑63 (MQ=255)
                      aCCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTg                                                <  1:1445341/71‑1 (MQ=255)
                        cTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTggg                                              >  1:161795/1‑71 (MQ=255)
                        cTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTggg                                              >  1:669612/1‑71 (MQ=255)
                          ttCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGgt                                            >  1:1575891/1‑71 (MQ=255)
                          ttCTGGTCACGACCGTGCATCGGGTTAGCACCCGGGCCGAACGGCGCGCCAGCacgac                                                         <  1:3335825/58‑1 (MQ=255)
                           tgcggTCACGACCATGCATCGGGTTAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCgt                                            <  1:3566356/67‑1 (MQ=255)
                           tCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGTCGCGCCAGCACGACGACCGTCTgggg                                             <  1:3913036/69‑1 (MQ=255)
                           tCTGGTCACGACCGCGCATCGGCTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTgggg                                             <  1:3622849/69‑1 (MQ=255)
                               gTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTa                                        <  1:319054/70‑1 (MQ=255)
                               gTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTa                                        <  1:3237536/70‑1 (MQ=255)
                               gTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTAc                                       >  1:1344474/1‑71 (MQ=255)
                               gTCACGACCATGCATCGGGTTAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTAc                                       <  1:802030/71‑1 (MQ=255)
                                tCACGACCATGCATCGGGTTAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTa                                        >  1:3712209/1‑69 (MQ=255)
                                  aCGACCATGCATCGGGTTAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTAccgg                                    >  1:2130713/1‑69 (MQ=255)
                                    gACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGtt                                  >  1:2110747/1‑71 (MQ=255)
                                      ccGTGCATCGGGTTAGCACCCGGTCCGAACGgcgcgc                                                                  >  1:2313018/1‑37 (MQ=255)
                                      ccGTGCATCGGGTTAGCACCCGGTCCGAACGgcgcgc                                                                  >  1:271689/1‑37 (MQ=255)
                                        atGCATCGGGTTAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCt                              <  1:2165478/70‑1 (MQ=255)
                                         tGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCtt                             <  1:2506416/71‑1 (MQ=255)
                                           cATCGGGTTAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCtggc                           <  1:536931/71‑4 (MQ=255)
                                           cATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTAc                           >  1:186636/1‑71 (MQ=255)
                                            aTCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTa                            >  1:1333899/1‑69 (MQ=255)
                                             tCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGgt                                            >  1:1597242/1‑52 (MQ=255)
                                             tCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                         <  1:2027753/71‑1 (MQ=255)
                                             tCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                         <  1:1570096/71‑1 (MQ=255)
                                              cGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                         >  1:3414294/1‑70 (MQ=255)
                                              cGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                         >  1:477167/1‑70 (MQ=255)
                                                  ttAGCGCCCGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTacac                    >  1:1069453/1‑71 (MQ=255)
                                                  ttAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTAccc                                     <  1:2251354/54‑1 (MQ=255)
                                                   tAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTggg                                              >  1:2723754/1‑44 (MQ=255)
                                                   tAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATacac                    >  1:3024232/1‑70 (MQ=255)
                                                     gCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAAc                 >  1:3832078/1‑71 (MQ=255)
                                                     gCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAAc                 <  1:3354176/71‑1 (MQ=255)
                                                        cccGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGtt              <  1:1391101/71‑1 (MQ=255)
                                                        cccGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGt               >  1:2929608/1‑70 (MQ=255)
                                                         ccGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTa                            <  1:2315160/56‑1 (MQ=255)
                                                         ccGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGt               >  1:3540482/1‑69 (MQ=255)
                                                            gTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAAc                 <  1:435448/64‑1 (MQ=255)
                                                            gTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAg            >  1:3297967/1‑69 (MQ=255)
                                                             tCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACAATACACaa                  >  1:2691225/1‑62 (MQ=255)
                                                               cGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACAGGTTTTCTGGCCGTACACCACGTTAGAAGt        <  1:1287419/70‑1 (MQ=255)
                                                               cGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGt        >  1:1936727/1‑70 (MQ=255)
                                                                gAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGa      >  1:3005560/1‑71 (MQ=255)
                                                                gAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                         <  1:303295/52‑1 (MQ=255)
                                                                gAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGa      <  1:2975766/71‑1 (MQ=255)
                                                                  aCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATg    >  1:1373502/1‑71 (MQ=255)
                                                                  aCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATg    >  1:2005067/1‑71 (MQ=255)
                                                                  aCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATg    >  1:2077016/1‑71 (MQ=255)
                                                                   cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATg    >  1:2907238/1‑70 (MQ=255)
                                                                    ggCGCGCCAGCACGACGACCGTCTGGGGTCTTACCCGTTTTCTTACCATacac                    <  1:273582/53‑1 (MQ=255)
                                                                      cgcgcCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGt  >  1:2267719/1‑69 (MQ=255)
                                                                      cgcgcCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGt  >  1:3077494/1‑69 (MQ=255)
                                                                      |                                                                    
CGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGT  >  minE/608300‑608438

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