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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,998,999 G→A 40.8% intergenic (‑452/‑2) ygeR ← / → xdhA Tetratricopeptide repeat transcriptional regulator/xanthine dehydrogenase, molybdenum binding subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,998,9990GA40.8% 30.7 / 56.4 49intergenic (‑452/‑2)ygeR/xdhATetratricopeptide repeat transcriptional regulator/xanthine dehydrogenase, molybdenum binding subunit
Reads supporting (aligned to +/- strand):  ref base G (14/15);  new base A (10/10);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01

TAAGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGATTATGTTATGG  >  W3110S.gb/2998929‑2999064
                                                                      |                                                                 
tAAGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcatg                                                                   <  1:3093346/71‑1 (MQ=255)
tAAGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcatg                                                                   <  1:719792/71‑1 (MQ=255)
tAAGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcatg                                                                   >  1:1855985/1‑71 (MQ=255)
  aGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcatgca                                                                 >  1:4625215/1‑71 (MQ=255)
  aGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcataca                                                                 >  1:4651741/1‑71 (MQ=255)
  aGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcataca                                                                 <  1:1604840/71‑1 (MQ=255)
  aGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcataca                                                                 >  1:4671063/1‑71 (MQ=255)
            gTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGa                                                       >  1:1893351/1‑71 (MQ=255)
               cAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCatacatgc                                                              >  1:573125/1‑61 (MQ=255)
                aaaTCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGcc                                                   <  1:1745845/71‑1 (MQ=255)
                aaaTCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGc                                                    >  1:406387/1‑70 (MQ=255)
                     gAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGc                                              <  1:2017203/71‑1 (MQ=255)
                       ggggATTTCTATGGAAGCTCGGGAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCt                                             <  1:1237549/70‑1 (MQ=255)
                       ggggATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTa                                            <  1:2286230/71‑1 (MQ=255)
                          gATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAgg                                         >  1:3397007/1‑71 (MQ=255)
                            tttCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGt                                        >  1:3712353/1‑70 (MQ=255)
                            tttCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGt                                        >  1:898961/1‑70 (MQ=255)
                             ttCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCa                                      >  1:3449748/1‑71 (MQ=255)
                             ttCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCa                                      >  1:495868/1‑71 (MQ=255)
                              tCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcatgca                                                                 <  1:4237325/43‑1 (MQ=255)
                              tCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATcatgca                                                                 >  1:803298/1‑43 (MQ=255)
                              tCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCa                                      <  1:3346808/70‑1 (MQ=255)
                              tCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCAc                                     >  1:4377049/1‑71 (MQ=255)
                                tATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGcc                                                   <  1:2594366/55‑1 (MQ=255)
                                    gAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACcgggcg                               >  1:4459088/1‑71 (MQ=255)
                                         gcgGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCAc                          >  1:4206242/1‑71 (MQ=255)
                                           gggAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGa                        <  1:382570/71‑1 (MQ=255)
                                           gggAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCAc                          <  1:4945336/69‑1 (MQ=255)
                                           gggAAGCAACCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGa                        <  1:4986434/71‑1 (MQ=255)
                                            ggAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGa                        <  1:193680/70‑1 (MQ=255)
                                             gAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTa                                            >  1:3645182/1‑49 (MQ=255)
                                             gAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGata                      >  1:5147170/1‑71 (MQ=255)
                                             gAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGata                      >  1:5141564/1‑71 (MQ=255)
                                             gAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGata                      <  1:4863775/71‑1 (MQ=255)
                                             gAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGata                      <  1:3028389/71‑1 (MQ=255)
                                                gCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATAc                   <  1:1167539/71‑1 (MQ=255)
                                                 cAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACt                  <  1:4136677/71‑1 (MQ=255)
                                                 cAACCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGa                        <  1:3359269/65‑1 (MQ=255)
                                                  aaCCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACt                  <  1:4328446/70‑1 (MQ=255)
                                                   aCCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTgc                >  1:1091247/1‑70 (MQ=255)
                                                   aCCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTa                                            <  1:2848252/43‑1 (MQ=255)
                                                   aCCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTa                                            <  1:2891196/43‑1 (MQ=255)
                                                   aCCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCAcc                                    >  1:711603/1‑51 (MQ=255)
                                                   aCCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCAcc                                    >  1:2599175/1‑51 (MQ=255)
                                                   aCCGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCAcc                                    >  1:2936428/1‑51 (MQ=255)
                                                     cGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGAc               >  1:1484834/1‑70 (MQ=255)
                                                     cGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGAc               >  1:488361/1‑70 (MQ=255)
                                                     cGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACg              <  1:845968/71‑1 (MQ=255)
                                                     cGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACg              <  1:4939961/71‑1 (MQ=255)
                                                     cGCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTaa                                           >  1:4574599/1‑42 (MQ=255)
                                                      gCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGa             <  1:1113700/71‑1 (MQ=255)
                                                      gCTACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGAtata                    >  1:4180126/1‑64 (MQ=255)
                                                        tACGGGTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGAt            >  1:4112705/1‑70 (MQ=255)
                                                            ggTGAATCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGAttatgt       <  1:3441145/71‑1 (MQ=255)
                                                             gTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGAttatgtt      <  1:2038183/71‑1 (MQ=255)
                                                              tGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGata                      <  1:3064022/54‑1 (MQ=255)
                                                               gAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGata                      >  1:1948791/1‑53 (MQ=255)
                                                                 aTCATACATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGATTATGTTATgg  >  1:4697441/1‑71 (MQ=255)
                                                                  tCATACATGCGCGTCGATGTCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGAttatgttat    <  1:3695355/68‑1 (MQ=255)
                                                                   catgcatgCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGAttatgttat    <  1:2917334/67‑1 (MQ=255)
                                                                      |                                                                 
TAAGAACCAAATGTTCAAATCGAGGGGATTTCTATGGAAGCGCGGGAAGCAACCGCTACGGGTGAATCATGCATGCGCGTCGATGCCATTGCTAAGGTCACCGGGCGGGCACGATATACTGACGATTATGTTATGG  >  W3110S.gb/2998929‑2999064

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