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
A5 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,836,867 A→G 8.7% K206K (AAA→AAG)  rfaB → UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,836,8670AG 8.7% 118.2 / 4.5 46K206K (AAA→AAG) rfaBUDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase
Reads supporting (aligned to +/- strand):  ref base A (17/25);  new base G (2/2);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

CCCGAGGAAGGTGAAACGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTCCGATT  >  W3110S.gb/3836796‑3836937
                                                                       |                                                                      
cccGAGGAAGGTGAAACGGCAACGTTTA‑TTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTaaa                                                                        <  1:613770/71‑1 (MQ=255)
  cGAGGAAGGTGAAACGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAg                                                                       <  1:1975910/71‑1 (MQ=255)
   gAGGAAGGTGAAACGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGa                                                                      >  1:3980878/1‑71 (MQ=255)
        aGGTGAAACGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGc                                                                 >  1:231947/1‑71 (MQ=255)
              aaCGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATg                                                           <  1:3613925/71‑1 (MQ=255)
              aaCGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATg                                                           >  1:1678600/1‑71 (MQ=255)
               aCGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATgg                                                          <  1:2307670/71‑1 (MQ=255)
                       gTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATcac                                                  <  1:4058308/71‑1 (MQ=255)
                        tttatttaTGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTaaa                                                                        <  1:336426/48‑1 (MQ=255)
                        tttatttaTGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATcaca                                                 <  1:2928742/71‑1 (MQ=255)
                        tttatttaTGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATcac                                                  >  1:652376/1‑70 (MQ=255)
                          tatttatGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCGTGATGGCTTa                                                      >  1:3055159/1‑64 (MQ=255)
                            tttatGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGc                                                                 >  1:3194250/1‑51 (MQ=255)
                               atGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGaa                                           <  1:3554009/70‑1 (MQ=255)
                                  ttGGGCGTATGAAATTTGAAGGACAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACaa                                                >  1:3864818/1‑62 (MQ=255)
                                   tGGGAGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGt                                       <  1:510003/70‑1 (MQ=255)
                                     ggCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGAt                                                            >  1:368970/1‑47 (MQ=255)
                                     ggCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTaa                                     <  1:732428/70‑1 (MQ=255)
                                     ggCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTaa                                     <  1:1502813/70‑1 (MQ=255)
                                     ggCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAAc                                    <  1:2123743/71‑1 (MQ=255)
                                         tATGAAATTTGAAGGCCAGAAAAGAGTTAAGGACCTGCtt                                                               <  1:1398618/40‑1 (MQ=255)
                                         tATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGa                                <  1:4017822/71‑1 (MQ=255)
                                         tATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGa                                <  1:1306894/71‑1 (MQ=255)
                                           tGAAATTTGAAGGCCAGAAAAGAGTTAAGGACCTGCTTGa                                                             >  1:3103991/1‑40 (MQ=255)
                                           tGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGt                                       <  1:110717/62‑1 (MQ=255)
                                            gAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAAc                             >  1:3215086/1‑71 (MQ=255)
                                             aaaTTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATca                                                   >  1:123469/1‑48 (MQ=255)
                                             aaaTTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACt                            >  1:395324/1‑71 (MQ=255)
                                             aaaTTTGAAGGCCAGAAAAGAGTTAAAGACC‑‑‑‑TGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCa                         <  1:3076573/70‑1 (MQ=255)
                                               aTTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTcc                          <  1:1766680/71‑1 (MQ=255)
                                               aTTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTc                           <  1:3910943/70‑1 (MQ=255)
                                                tttGAAGGCCAGAAAAGAGTTAAACACCTGCTTGATGGCTTATCACaa                                                <  1:102550/48‑1 (MQ=255)
                                                  tGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGc                                                         >  1:1767546/1‑37 (MQ=255)
                                                   gAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATg                       <  1:1871485/70‑1 (MQ=255)
                                                    aaGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGt                      <  1:263929/70‑1 (MQ=255)
                                                    aaGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGt                      <  1:2414610/70‑1 (MQ=255)
                                                        ccAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGa                                <  1:2439766/56‑1 (MQ=255)
                                                        ccAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTgg                 <  1:1410940/71‑1 (MQ=255)
                                                         cAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTgg                 >  1:1917064/1‑70 (MQ=255)
                                                           gAAAAGAGTTAAGGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGt               >  1:2083359/1‑70 (MQ=255)
                                                           gAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGt               >  1:2806998/1‑70 (MQ=255)
                                                            aaaaGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAg                                         <  1:3535024/43‑1 (MQ=255)
                                                             aaaGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGAt            >  1:2582447/1‑71 (MQ=255)
                                                                gagTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGc         <  1:3112805/71‑1 (MQ=255)
                                                                   ttAAGGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGt               <  1:1016591/62‑1 (MQ=255)
                                                                   ttAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTAt                    >  1:1808994/1‑57 (MQ=255)
                                                                   ttAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTcc      <  1:3587718/71‑1 (MQ=255)
                                                                    tAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGaaa                              >  1:1529956/1‑46 (MQ=255)
                                                                     aaaGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTcc                          >  1:3054874/1‑49 (MQ=255)
                                                                     aaaGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCa                         >  1:377073/1‑50 (MQ=255)
                                                                     aaaGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCa                         >  1:2118309/1‑50 (MQ=255)
                                                                     aaaGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTCCg     <  1:19823/70‑1 (MQ=255)
                                                                     aaaGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTCCGa    >  1:1592486/1‑71 (MQ=255)
                                                                      aaGACCTGTTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTCCGa    <  1:621229/70‑1 (MQ=255)
                                                                       aGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAAc                                    >  1:3982180/1‑37 (MQ=255)
                                                                       aGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAAc                                    >  1:2772383/1‑37 (MQ=255)
                                                                       aGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTg                  <  1:3774677/55‑1 (MQ=255)
                                                                       aGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTCCGAtt  <  1:3775660/71‑1 (MQ=255)
                                                                       |                                                                      
CCCGAGGAAGGTGAAACGGCAACGTTTATTTATGTTGGGCGTATGAAATTTGAAGGCCAGAAAAGAGTTAAAGACCTGCTTGATGGCTTATCACAAGCGAAAGGTAACTGGAAACTCCATGTATTGGGTGATGGCTCCGATT  >  W3110S.gb/3836796‑3836937

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