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
A1 F999 I1 R1 225 156.4 11709729 83.8% 9812752 75.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,510,121 +G intergenic (‑358/+151) yhfZ ← / ← trpS hypothetical protein/tryptophan tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,510,1201.G96.4% 211.6 / 2.7 84intergenic (‑357/+152)yhfZ/trpShypothetical protein/tryptophan tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base G (51/29);  total (51/33)
Fisher's exact test for biased strand distribution p-value = 5.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

GAGATGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑GTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAAT  >  NC_000913/3510046‑3510190
                                                                            |                                                                      
gagaTGTGGAAACGGCGAGGCACTTCACAGTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGCTTC‑CCC‑g                                                                       >  1:1665620/1‑76 (MQ=255)
 agaTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑gg                                                                      >  2:2570013/1‑75 (MQ=255)
 agaTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑gg                                                                      >  1:3053577/1‑75 (MQ=255)
 agaTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑gg                                                                      <  2:4034266/76‑2 (MQ=255)
   aTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGGGGATAAAAAAACCGGGTTTC‑CCC‑ggtt                                                                    <  2:3623376/76‑4 (MQ=255)
   aTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑ggtt                                                                    >  1:5200779/1‑73 (MQ=255)
   aTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑ggtt                                                                    <  1:2747591/76‑4 (MQ=255)
   aTGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑ggtt                                                                    >  1:5174696/1‑73 (MQ=255)
       ggAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCag                                                                 >  1:4600316/1‑76 (MQ=255)
        gAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCaga                                                                >  2:1540152/1‑76 (MQ=255)
          aaCGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGt                                                              <  1:3045396/76‑1 (MQ=255)
          aaCGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGt                                                              <  1:495169/76‑1 (MQ=255)
           aCGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGtg                                                             <  1:1051224/76‑1 (MQ=255)
            cGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGtga                                                            >  1:1232292/1‑76 (MQ=255)
             ggCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGtgat                                                           <  2:1094379/76‑1 (MQ=255)
              gCGAGGCAGTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGtgatc                                                          >  2:2049893/1‑75 (MQ=255)
              gCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGtgatg                                                          >  2:3948940/1‑76 (MQ=255)
                 aGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATa                                                       >  2:5264717/1‑76 (MQ=255)
                   gCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATaaa                                                     <  2:460859/76‑1 (MQ=255)
                    cACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATaaaa                                                    >  1:4921836/1‑76 (MQ=255)
                    cACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATaaaa                                                    >  2:1930310/1‑76 (MQ=255)
                     aCTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAg                                                   >  1:2224093/1‑76 (MQ=255)
                      cTTCACACTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGc                                                  <  1:3956157/76‑1 (MQ=255)
                       ttCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCa                                                 >  1:3636900/1‑76 (MQ=255)
                       ttCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCa                                                 <  1:5771408/76‑1 (MQ=255)
                        tCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCaa                                                <  2:2265150/76‑1 (MQ=255)
                        tCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCaa                                                >  1:1099175/1‑76 (MQ=255)
                          acaTTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCaaaa                                              >  2:2633182/1‑76 (MQ=255)
                          acaTTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCaaaa                                              <  1:267050/76‑1 (MQ=255)
                           caTTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAAt                                             >  1:3473021/1‑76 (MQ=255)
                            aTTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAAtt                                            <  1:3837559/76‑1 (MQ=255)
                             ttttttCGGATTATTGCAAATGAGGAT‑AAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGc                                          >  2:1643095/1‑76 (MQ=255)
                              tttttCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGc                                          >  1:4790522/1‑76 (MQ=255)
                               ttttCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGcc                                         <  1:1189200/76‑1 (MQ=255)
                               ttttCGGATTATTGCAAATGAGGATAAAAAAACCGGGGTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGcc                                         >  1:5777848/1‑76 (MQ=255)
                                 ttCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTg                                       <  1:343873/76‑1 (MQ=255)
                                  tCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGa                                      >  2:2265941/1‑76 (MQ=255)
                                  tCGGACTATTGAAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCACAGTGATGATAAAAGCAAAATTGCCTGa                                      >  2:4011378/1‑76 (MQ=255)
                                   cGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGAt                                     >  1:3419179/1‑76 (MQ=255)
                                   cGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGAt                                     <  2:4243257/76‑1 (MQ=255)
                                   cGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGAt                                     >  2:4736048/1‑76 (MQ=255)
                                     gATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATgc                                   >  1:3906639/1‑76 (MQ=255)
                                      attattGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATgcg                                  >  2:286072/1‑76 (MQ=255)
                                       ttattGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATgcgc                                 >  1:4614971/1‑76 (MQ=255)
                                         attGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTa                               >  2:3258614/1‑76 (MQ=255)
                                          ttGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTAc                              >  2:2672518/1‑76 (MQ=255)
                                          ttGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTAc                              >  2:639628/1‑76 (MQ=255)
                                          ttGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTAc                              >  2:5175001/1‑76 (MQ=255)
                                          ttGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTAc                              <  2:1218413/76‑1 (MQ=255)
                                           tGCAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACg                             >  1:5713366/1‑76 (MQ=255)
                                             cAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCt                           <  1:3920675/76‑1 (MQ=255)
                                             cAAATGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCt                           <  1:5417816/76‑1 (MQ=255)
                                              aaaTGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCtt                          >  2:2931291/1‑76 (MQ=255)
                                               aaTGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTa                         >  2:1360427/1‑76 (MQ=255)
                                               aaTGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTa                         <  1:2530116/76‑1 (MQ=255)
                                                aTGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTAt                        >  1:556783/1‑76 (MQ=255)
                                                 tGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATc                       <  2:1738320/76‑1 (MQ=255)
                                                 tGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATc                       >  2:5190899/1‑76 (MQ=255)
                                                 tGAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATc                       >  2:801782/1‑76 (MQ=255)
                                                  gAGGATAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCa                      <  1:3290226/76‑1 (MQ=255)
                                                     gATAAAAAAACCGGGTCTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGAGGCGCTACGCTTATCAGGc                   >  2:2833366/1‑76 (MQ=25)
                                                      aTAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGcc                  <  2:1665620/76‑1 (MQ=255)
                                                      aTAAAAAAACCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGcc                  >  1:4958650/1‑76 (MQ=255)
                                                         aaaaaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTAc               >  2:1779282/1‑76 (MQ=255)
                                                         aaaaaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTAc               >  1:4542799/1‑76 (MQ=255)
                                                          aaaaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACa              >  2:941255/1‑76 (MQ=255)
                                                           aaaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAt             <  2:5098440/76‑1 (MQ=255)
                                                           aaaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAt             >  1:2792490/1‑76 (MQ=255)
                                                            aagccGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            <  1:1841111/73‑1 (MQ=21)
                                                            aaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            >  1:1264330/1‑76 (MQ=255)
                                                            aaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            <  1:1813668/76‑1 (MQ=255)
                                                            aaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            <  2:1374431/76‑1 (MQ=255)
                                                            aaaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            >  2:3164417/1‑76 (MQ=255)
                                                            aaaCCGGGTGTCACCG‑GTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            <  1:1841244/76‑1 (MQ=18)
                                                            aaaCCGGGTGTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            <  1:1841214/76‑1 (MQ=21)
                                                            aaaCCGGGTGTA‑CCAGGTGTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAtt            <  1:1841221/76‑1 (MQ=17)
                                                             aaCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAttt           >  2:5292414/1‑76 (MQ=255)
                                                              aCCTGGTTTC‑CTCTGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTCTCAGGCCTCCATTTc          <  1:599592/76‑1 (MQ=18)
                                                              aCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTc          >  2:163676/1‑76 (MQ=255)
                                                              aCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTc          >  1:2698028/1‑76 (MQ=255)
                                                              aCCGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTc          <  2:3359827/76‑1 (MQ=255)
                                                               ccGGGTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTcc         >  1:3759670/1‑76 (MQ=255)
                                                                 gggTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCtt       >  1:3427141/1‑76 (MQ=255)
                                                                 gggTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCtt       <  1:5190900/76‑1 (MQ=255)
                                                                  ggTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTg      >  2:1716162/1‑76 (MQ=255)
                                                                  ggTTCC‑CCG‑GTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGTCCTTGc     <  2:5200778/76‑1 (MQ=18)
                                                                   gTTTC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGc     <  2:5174695/76‑1 (MQ=255)
                                                                   gTTCC‑CCG‑GTTTCAGAGTGATTATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACGTTTCCTTGCa    <  2:3532045/76‑1 (MQ=18)
                                                                    tttC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCa    >  1:3058859/1‑76 (MQ=255)
                                                                    tttC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCa    >  2:1448702/1‑76 (MQ=255)
                                                                     ttC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCaa   >  1:676559/1‑76 (MQ=255)
                                                                      tC‑CCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAat  >  2:3720303/1‑76 (MQ=255)
                                                                            |                                                                      
GAGATGTGGAAACGGCGAGGCACTTCACATTTTTTCGGATTATTGCAAATGAGGATAAAAAAACCGGGTTTC‑CCC‑GTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAAT  >  NC_000913/3510046‑3510190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A