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 608,340 G→A 9.2% H638H (CAC→CAT)  pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE608,3400GA 9.2% 187.7 / 7.6 66H638H (CAC→CAT) pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base G (27/32);  new base A (3/3);  total (30/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01

TTTAGCGTAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTT  >  minE/608271‑608406
                                                                     |                                                                  
tttAGCGTAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGt                                                                   >  1:1980820/1‑71 (MQ=255)
  tAGCGTAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGTACCTTTCTGGTCACGACCGTg                                                                  >  1:87529/1‑70 (MQ=255)
     cGTAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATc                                                              <  1:3250035/71‑1 (MQ=255)
     cGTAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTAACGACCGTGc                                                                 <  1:913851/68‑1 (MQ=255)
     cGTAAGAAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATc                                                              <  1:3164314/71‑1 (MQ=255)
       tAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCgg                                                            >  1:1019022/1‑71 (MQ=255)
         aGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCATCTTTCTGGTCACGACCGTGCATCGGGt                                                          <  1:3696793/71‑1 (MQ=255)
         aGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGt                                                          >  1:850934/1‑71 (MQ=255)
         aGCAAACGGCAGTTTAGCAACGGAAGGCAGCGCGGCTACTGCACCTTTCTGGTCACGACCGTGCATCggg                                                           <  1:3344432/70‑1 (MQ=255)
          gtgaaCGGCAGTTTCGCCACCGACGTCAATGAGGCCACGGCACCTTTGCGGTCACGACCATGCATCGGGtt                                                         <  1:2517230/68‑1 (MQ=255)
          gCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCgg                                                            >  1:1086037/1‑68 (MQ=255)
          gCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGtt                                                         <  1:3646045/71‑1 (MQ=255)
             aaCGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATc                                                              <  1:1799456/63‑1 (MQ=255)
              aCGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCa                                                     <  1:552843/71‑1 (MQ=255)
               cGGCAGTTTCGCCACCGACGTCAATGAGGCCACGGCACCTTTGCGGTCACGACCATGCATCGGGTTAGcgc                                                    >  1:2072388/1‑69 (MQ=255)
                ggCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCAcc                                                   <  1:1770690/71‑1 (MQ=255)
                   aGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCgg                                                <  1:1867519/71‑1 (MQ=255)
                   aGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCgg                                                <  1:539325/71‑1 (MQ=255)
                    gTTTCGCCACCGACGTCAATGAGGCCACGGCACCTTTGCGGTCACGACCCTGCATCGGGTTAGCGCCCggc                                               <  1:3263540/71‑2 (MQ=255)
                     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)
                        aGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCAcc                                                   >  1:323299/1‑63 (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)
                                aaGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGc                                                      <  1:1505466/52‑1 (MQ=255)
                                aaGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGc                                                      <  1:751043/52‑1 (MQ=255)
                                 aGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGgcgcgc                                  >  1:779293/1‑71 (MQ=255)
                                  gTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCg                                                 <  1:2161746/55‑1 (MQ=255)
                                     agagagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGtt                                                         >  1:546803/1‑44 (MQ=255)
                                     agagagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCa                                <  1:1961746/69‑1 (MQ=255)
                                     agagagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGc                              <  1:2220336/71‑1 (MQ=255)
                                       agagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                            <  1:2923959/71‑1 (MQ=255)
                                        gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGtt                                                         <  1:506275/41‑1 (MQ=255)
                                        gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGaa                                          <  1:3905117/56‑1 (MQ=255)
                                        gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                            >  1:696155/1‑70 (MQ=255)
                                        gagGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCac                            >  1:1172352/1‑70 (MQ=255)
                                         agGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGt                                                          <  1:2689728/39‑1 (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              >  1:161795/1‑71 (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        <  1:3237536/70‑1 (MQ=255)
                                                            gTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTa        <  1:319054/70‑1 (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)
                                                                     |                                                                  
TTTAGCGTAAGCAAACGGCAGTTTAGCAACGGAAGTCAGAGAGGCTACTGCACCTTTCTGGTCACGACCGTGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTT  >  minE/608271‑608406

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