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 608,362 C→G 12.1% G631A (GGA→GCA) ‡ pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE608,3620CG12.1% 148.9 / 11.1 58G631A (GGA→GCA) ‡pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base C (27/24);  new base G (3/4);  total (30/28)
Fisher's exact test for biased strand distribution p-value = 7.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01

TTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAG  >  minE/608292‑608428
                                                                      |                                                                  
tttAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTc                                                                    >  1:3031956/1‑71 (MQ=255)
  tAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTcc                                                                   >  1:878034/1‑70 (MQ=255)
  tAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTcc                                                                   >  1:3643701/1‑70 (MQ=255)
  tAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTcc                                                                   >  1:2954541/1‑70 (MQ=255)
  tAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTc                                                                    >  1:2297856/1‑69 (MQ=255)
    gCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGa                                                                 <  1:1527459/70‑1 (MQ=255)
      aaCGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACg                                                              <  1:2364158/71‑1 (MQ=255)
       aCGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACgg                                                             >  1:3186160/1‑71 (MQ=255)
       aCGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACg                                                              <  1:3366397/70‑1 (MQ=255)
        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)
                   gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGaa                                                                <  1:3905117/56‑1 (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)
                          cTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCg                                                                  <  1:1299860/47‑1 (MQ=255)
                            gCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCacga                                                >  1:2314731/1‑63 (MQ=255)
                              aCCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTg                                      <  1:1445341/71‑1 (MQ=255)
                                cTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTggg                                    >  1:669612/1‑71 (MQ=255)
                                cTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTggg                                    >  1:161795/1‑71 (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                                                        >  1:271689/1‑37 (MQ=255)
                                              ccGTGCATCGGGTTAGCACCCGGTCCGAACGgcgcgc                                                        >  1:2313018/1‑37 (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               <  1:1570096/71‑1 (MQ=255)
                                                     tCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa               <  1:2027753/71‑1 (MQ=255)
                                                      cGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa               >  1:477167/1‑70 (MQ=255)
                                                      cGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa               >  1:3414294/1‑70 (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)
                                                                      |                                                                  
TTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAG  >  minE/608292‑608428

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