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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,283,783 G→T 24.0% L39M (CTG→ATG)  oxyR ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,283,7830GT24.0% 154.8 / 22.8 58L39M (CTG→ATG) oxyRDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base G (26/18);  new base T (2/12);  total (28/30)
Fisher's exact test for biased strand distribution p-value = 4.99e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

TTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGC  >  minE/2283714‑2283851
                                                                     |                                                                    
ttCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGc                                                                     >  1:266468/1‑71 (MQ=255)
ttCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGc                                                                     >  1:463161/1‑71 (MQ=255)
  cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAg                                                                      >  1:3036929/1‑68 (MQ=255)
  cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCt                                                                    <  1:636302/70‑1 (MQ=255)
  cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCt                                                                    >  1:2374714/1‑70 (MQ=255)
   ccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCtt                                                                   <  1:2065336/70‑1 (MQ=255)
     gCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACg                                                                <  1:337629/71‑1 (MQ=255)
     gCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACg                                                                <  1:2801168/71‑1 (MQ=255)
      ccTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGa                                                               <  1:469118/71‑1 (MQ=255)
      ccTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGa                                                               <  1:3967384/71‑1 (MQ=255)
       cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa                                                              <  1:546291/71‑1 (MQ=255)
       cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa                                                              <  1:2623357/71‑1 (MQ=255)
       cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa                                                              <  1:2472279/71‑1 (MQ=255)
       cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGa                                                               <  1:2304735/70‑1 (MQ=255)
       cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGa                                                               <  1:3485474/70‑1 (MQ=255)
          ggTGAACAACACTTTACGGCTTGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAAtt                                                            <  1:2637655/70‑1 (MQ=255)
          ggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAttt                                                           <  1:2944256/71‑1 (MQ=255)
          ggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAttt                                                           <  1:1566960/71‑1 (MQ=255)
          ggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAttt                                                           <  1:1452820/71‑1 (MQ=255)
          ggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAttt                                                           <  1:218303/71‑1 (MQ=255)
                 aacaCTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCt                                                    <  1:632430/71‑1 (MQ=255)
                 aacaCTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCt                                                    <  1:49346/71‑1 (MQ=255)
                  acacTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTa                                                   <  1:3328813/71‑1 (MQ=255)
                     cTTTACGGCTTGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGATAAGc                                                <  1:2087250/71‑1 (MQ=255)
                     cTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGATAAGc                                                <  1:61223/71‑1 (MQ=255)
                     cTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGATAAGc                                                <  1:1725101/71‑1 (MQ=255)
                        tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAg                                                 >  1:610513/1‑67 (MQ=255)
                        tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAg                                                 >  1:1774771/1‑67 (MQ=255)
                                gTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCggctggct                                     <  1:2535909/71‑1 (MQ=255)
                                  ccGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTaa                                   >  1:2182498/1‑71 (MQ=255)
                                     cTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:2397176/71‑1 (MQ=255)
                                     cTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:3849316/71‑1 (MQ=255)
                                     cTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:74742/71‑1 (MQ=255)
                                        cAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCggctggct                                     >  1:1837072/1‑63 (MQ=255)
                                        cAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTgg                              >  1:2934284/1‑70 (MQ=255)
                                          gCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAt                                                             >  1:580894/1‑37 (MQ=255)
                                          gCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAt                                                             >  1:2495383/1‑37 (MQ=255)
                                          gCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAt                                                             >  1:3309404/1‑37 (MQ=255)
                                          gCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAt                                                             >  1:2300349/1‑37 (MQ=255)
                                          gCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAt                                                             >  1:1193937/1‑37 (MQ=255)
                                             aCATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGa                         >  1:56553/1‑70 (MQ=255)
                                               aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                >  1:1973091/1‑61 (MQ=255)
                                               aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGan                        >  1:2464969/1‑68 (MQ=255)
                                               aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAAt                       >  1:3120234/1‑70 (MQ=255)
                                               aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAAt                       >  1:1698813/1‑70 (MQ=255)
                                               aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAAt                       >  1:151248/1‑70 (MQ=255)
                                                  aCGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGc                   >  1:2383089/1‑71 (MQ=255)
                                                  aCGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGc                   <  1:816479/71‑1 (MQ=255)
                                                         gCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:129745/51‑1 (MQ=255)
                                                               cTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGaaaa      >  1:2020715/1‑71 (MQ=255)
                                                                ttCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAt     >  1:3975913/1‑71 (MQ=255)
                                                                ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATc                      >  1:3722423/1‑54 (MQ=255)
                                                                ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATc                      >  1:2692164/1‑54 (MQ=255)
                                                                ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAt     >  1:440910/1‑71 (MQ=255)
                                                                ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAt     >  1:2777804/1‑71 (MQ=255)
                                                                ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAt     >  1:1714175/1‑71 (MQ=255)
                                                                  ccAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATgg   >  1:44950/1‑71 (MQ=255)
                                                                   cAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGc  <  1:2066098/71‑1 (MQ=255)
                                                                   cAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGc  <  1:676859/71‑1 (MQ=255)
                                                                     |                                                                    
TTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGC  >  minE/2283714‑2283851

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