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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,453,265 C→T pseudogene (1737/2646 nt) yfcU ← pseudogene, FimD fimbrial export usher family,putative membrane, Not classified, putative outer membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,453,2650CT98.5% 209.3 / NA 65pseudogene (1737/2646 nt)yfcUpseudogene, FimD fimbrial export usher family,putative membrane, Not classified, putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (28/36);  minor base G (0/1);  total (28/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATCTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGATCC  >  NC_000913/2453138‑2453397
                                                                                                                               |                                                                                                                                    
tCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   <  2:867344/131‑1 (MQ=255)
tCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   >  1:867344/1‑131 (MQ=255)
      gATAGTGAGTCGCGTCAACGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGc                                                                                                                     >  1:782513/1‑139 (MQ=255)
       aTAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGcc                                                                                                                    >  1:1192433/1‑139 (MQ=255)
        tAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCG‑CCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCg                                                                                                                  <  2:428708/139‑1 (MQ=255)
           tGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   <  1:1038838/120‑1 (MQ=255)
           tGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   >  2:1038838/1‑120 (MQ=255)
              gTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGt                                                                                                             >  1:1107705/1‑139 (MQ=255)
              gTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGt                                                                                                             >  1:85259/1‑139 (MQ=255)
                 gcgTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCAt                                                                                                          <  2:85259/139‑1 (MQ=255)
                 gcgTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCAt                                                                                                          >  1:374358/1‑139 (MQ=255)
                       tCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGt                                                                                                    >  1:274890/1‑139 (MQ=255)
                               gCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            <  2:527486/139‑1 (MQ=255)
                               gCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            <  2:1107705/139‑1 (MQ=255)
                                    aaTAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGt                                                                                       <  2:1192433/139‑1 (MQ=255)
                                        aCCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCg                                                                                                     <  2:1368946/121‑1 (MQ=255)
                                        aCCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCg                                                                                                     >  1:1368946/1‑121 (MQ=255)
                                          cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGccc                                                                                                                   >  1:367122/1‑105 (MQ=255)
                                          cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGccc                                                                                                                   <  2:367122/105‑1 (MQ=255)
                                          cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            >  1:368487/1‑128 (MQ=255)
                                          cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            <  2:368487/128‑1 (MQ=255)
                                          cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGa                                                                                 <  2:1087920/139‑1 (MQ=255)
                                          cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGa                                                                                 <  2:274890/139‑1 (MQ=255)
                                                           gtccCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                           >  2:303665/1‑128 (MQ=255)
                                                           gtccCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                           <  1:303665/128‑1 (MQ=255)
                                                             cccACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAAtg                                                              <  2:38066/139‑1 (MQ=255)
                                                              ccACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAAtgc                                                             <  1:239504/139‑1 (MQ=255)
                                                                aCTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCATGGCATACTGAGCGAAATGTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAAtcctg                                                           <  1:880228/139‑1 (MQ=255)
                                                                  tGCTATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  2:94556/139‑1 (MQ=255)
                                                                  tGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  1:511144/139‑1 (MQ=255)
                                                                  tGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  2:782513/139‑1 (MQ=255)
                                                                  tGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  2:1193152/139‑1 (MQ=255)
                                                                    ccATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCa                                                       <  2:374358/139‑1 (MQ=255)
                                                                       tAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  2:534229/134‑1 (MQ=255)
                                                                       tAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         >  1:534229/1‑134 (MQ=255)
                                                                         gTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACa                                                                                                                                  <  1:672677/59‑1 (MQ=255)
                                                                         gTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACa                                                                                                                                  >  2:672677/1‑59 (MQ=255)
                                                                            gCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCg                                                                                                     <  2:1288639/85‑1 (MQ=255)
                                                                            gCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCg                                                                                                     >  1:1288639/1‑85 (MQ=255)
                                                                            gCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTAc                                                                   >  2:1210446/1‑119 (MQ=255)
                                                                            gCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTAc                                                                   <  1:1210446/119‑1 (MQ=255)
                                                                              cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         >  2:161629/1‑127 (MQ=255)
                                                                              cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  1:161629/127‑1 (MQ=255)
                                                                                             tACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGa                                                                                 >  2:953439/1‑88 (MQ=255)
                                                                                             tACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGa                                                                                 <  1:953439/88‑1 (MQ=255)
                                                                                               cTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                           <  2:909584/92‑1 (MQ=255)
                                                                                               cTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                           >  1:909584/1‑92 (MQ=255)
                                                                                                tgttgtCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGAtgtt                           <  2:357406/139‑1 (MQ=255)
                                                                                                     tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTc                                                                                                            >  1:692043/1‑53 (MQ=255)
                                                                                                     tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTc                                                                                                            <  2:692043/53‑1 (MQ=255)
                                                                                                     tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGt                      >  2:766268/1‑139 (MQ=255)
                                                                                                     tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGt                      >  2:750322/1‑139 (MQ=255)
                                                                                                       gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGt                                                                                                             >  2:192851/1‑50 (MQ=255)
                                                                                                       gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGt                                                                                                             <  1:192851/50‑1 (MQ=255)
                                                                                                       gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCat                                 <  1:780314/126‑1 (MQ=255)
                                                                                                       gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCat                                 >  2:780314/1‑126 (MQ=255)
                                                                                                         cccACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         <  2:514383/100‑1 (MQ=255)
                                                                                                         cccACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                         >  1:514383/1‑100 (MQ=255)
                                                                                                                     tGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACg      <  2:272688/139‑1 (MQ=255)
                                                                                                                        gCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGa                                                 <  2:829111/93‑1 (MQ=255)
                                                                                                                        gCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGa                                                 >  1:829111/1‑93 (MQ=255)
                                                                                                                         cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            <  2:862473/49‑1 (MQ=255)
                                                                                                                         cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            >  1:862473/1‑49 (MQ=255)
                                                                                                                         cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGATcc  >  2:416541/1‑139 (MQ=255)
                                                                                                                            aaTTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            <  1:850628/46‑1 (MQ=255)
                                                                                                                               |                                                                                                                                    
TCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATCTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGATCC  >  NC_000913/2453138‑2453397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A