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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,728,118 (C)8→9 coding (1254/1455 nt) xylB ← xylulokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,728,1101.C88.6% 135.9 / 9.7 44coding (1262/1455 nt)xylBxylulokinase
Reads supporting (aligned to +/- strand):  ref base . (2/3);  new base C (15/24);  total (17/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01

GGCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCA  >  NC_000913/3727972‑3728229
                                                                                                                                           |                                                                                                                        
ggCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAt                                                                                                                           >  2:704473/1‑139 (MQ=255)
 gCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑c                                                                                                                        >  2:1193590/1‑139 (MQ=255)
  cTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cc                                                                                                                       <  1:1479392/139‑1 (MQ=255)
  cTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cc                                                                                                                       <  1:1404014/139‑1 (MQ=255)
    gATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGTGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cccc                                                                                                                     <  1:1058293/139‑1 (MQ=255)
    gATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cccc                                                                                                                     <  1:66512/139‑1 (MQ=255)
     aTAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑ccccc                                                                                                                    <  2:1258401/139‑1 (MQ=255)
     aTAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑ccccc                                                                                                                    <  2:1064792/139‑1 (MQ=255)
       aaGGGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑ccccccc                                                                                                                  <  2:1039881/139‑1 (MQ=255)
            gCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cccccccccgta                                                                                                             >  2:832606/1‑135 (MQ=255)
             cATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cccccccccgtac                                                                                                            >  1:913699/1‑134 (MQ=255)
               tAACGCTGCGCATCTGGTAAATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACgg                                                                                                           >  1:1093547/1‑139 (MQ=255)
                     tGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCg                                                                                                     <  1:704473/139‑1 (MQ=255)
                            cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAgctgct                                                                                              <  2:888468/139‑1 (MQ=255)
                            cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAgctgct                                                                                              >  2:470942/1‑139 (MQ=255)
                            cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAgctgct                                                                                              >  2:393085/1‑139 (MQ=255)
                            cTGGTAAATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAgctgct                                                                                              <  2:1093547/139‑1 (MQ=255)
                                     gCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGa                                                                                     <  2:1322688/139‑1 (MQ=255)
                                         cTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATcc                                                                                >  1:1019214/1‑139 (MQ=255)
                                             tCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGcc                                                                             >  2:452547/1‑139 (MQ=255)
                                                    gTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCt                                                                      <  1:832606/139‑1 (MQ=255)
                                                    gTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCt                                                                      <  2:1084788/139‑1 (MQ=255)
                                                      aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGAc                                                                   <  2:1019214/139‑1 (MQ=255)
                                                        ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCAt                                                                        >  1:767527/1‑133 (MQ=255)
                                                        ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCAt                                                                        <  2:767527/133‑1 (MQ=255)
                                                        ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                  <  1:809667/139‑1 (MQ=255)
                                                        ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                  <  2:913699/139‑1 (MQ=255)
                                                           cGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCa                                                               <  1:1193590/139‑1 (MQ=255)
                                                              caacaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTa                                                            <  2:120576/139‑1 (MQ=255)
                                                               aacaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCCCCCCCGTAATCGAGCTGCTCCCCGCTGATATCCCCCCCCCCCTGACGCCCGtc                                                            >  1:1334571/1‑138 (MQ=255)
                                                                acaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACt                                                          <  1:1272796/139‑1 (MQ=255)
                                                                            gCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAt                                                                                                                           <  1:895803/63‑1 (MQ=255)
                                                                            gCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAt                                                                                                                           >  2:895803/1‑63 (MQ=255)
                                                                                  tctcTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccccgccc                                         <  2:1265055/139‑1 (MQ=255)
                                                                                     ctGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTTACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCaa                                     >  1:581175/1‑139 (MQ=255)
                                                                                      tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                    <  2:1199580/139‑1 (MQ=255)
                                                                                      tGGATTCGCCGCGATCTGCGCCAGCCTCGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCCTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                    >  2:580080/1‑139 (MQ=255)
                                                                                           tCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACg                               >  2:185424/1‑139 (MQ=255)
                                                                                            cgccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACg                               <  2:1334571/139‑1 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTaa                                                                                                        >  1:876069/1‑64 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTaa                                                                                                        <  2:876069/64‑1 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATTTCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTaa                            >  1:353178/1‑139 (MQ=255)
                                                                                              ccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgcccc                                             >  2:1194723/1‑122 (MQ=255)
                                                                                              ccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgcccc                                             <  1:1194723/122‑1 (MQ=255)
                                                                                               cgcgATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cccccccccgta                                                                                                             >  1:862480/1‑52 (MQ=255)
                                                                                               cgcgATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑cccccccccgta                                                                                                             <  2:862480/56‑5 (MQ=255)
                                                                                                    tCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                     <  2:353178/139‑1 (MQ=255)
                                                                                                      tGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGc                    <  1:728893/139‑1 (MQ=255)
                                                                                                      tGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAGTCAACGTAACACTTTGCg                   <  2:350751/139‑1 (MQ=255)
                                                                                                              ccTTGCTGCGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCCCCCCCAATCAACGTAACACTTTGCGGTTTAAt            >  1:607339/1‑139 (MQ=255)
                                                                                                                  gctgcGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCg        >  2:1246776/1‑139 (MQ=255)
                                                                                                                    tgcGCCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCa      <  1:1246776/139‑1 (MQ=255)
                                                                                                                     gcgcCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAg     <  1:470942/139‑1 (MQ=255)
                                                                                                                       gcCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCg                   <  2:1424141/123‑1 (MQ=255)
                                                                                                                       gcCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGc   <  1:452547/139‑1 (MQ=255)
                                                                                                                       gcCCAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGACATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCg                   >  1:1424141/1‑123 (MQ=255)
                                                                                                                        cccAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACt                                                          >  2:470758/1‑83 (MQ=255)
                                                                                                                        cccAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACt                                                          <  1:470758/83‑1 (MQ=255)
                                                                                                                        cccAGTGCTGGCCCCACATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCa  <  1:185424/139‑1 (MQ=255)
                                                                                                                                           |                                                                                                                        
GGCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCA  >  NC_000913/3727972‑3728229

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A