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
A6 F28 I1 R1 132 61.4 2079690 99.1% 2060972 139.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,162,335 G→A G291D (GGC→GAC)  mdtD → putative multidrug efflux pump MdtD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,162,3350GA98.2% 155.5 / ‑4.7 54G291D (GGC→GAC) mdtDputative multidrug efflux pump MdtD
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (31/22);  total (32/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01

CAGAAATAACAACCGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGGCCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGCGACCACGCTGGGT  >  NC_000913/2162198‑2162471
                                                                                                                                         |                                                                                                                                        
cAGAAATAACAACCGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGAcc                                                                                                                                        >  2:599475/1‑140 (MQ=255)
   aaaTAACAACCGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCg                                                                                                                                     >  2:516935/1‑140 (MQ=255)
     aTAACAACCGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGGATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGAACTCggg                                                                                                                                   >  1:954998/1‑139 (MQ=255)
             cGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGcc                                                                                                                           >  2:483476/1‑140 (MQ=255)
             cGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGcc                                                                                                                           >  1:497246/1‑140 (MQ=255)
              gTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGGGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGGTTCTCGCCg                                                                                                                          >  2:885005/1‑140 (MQ=255)
                 cccTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGttt                                                                                                                       >  1:422652/1‑140 (MQ=255)
                   cTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCa                                                                                                                     <  1:848508/140‑1 (MQ=255)
                     gTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATg                                                                                                                   <  2:383181/140‑1 (MQ=255)
                      ttCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGc                                                                                                                  <  2:162018/140‑1 (MQ=255)
                      ttCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGc                                                                                                                  >  1:407598/1‑140 (MQ=255)
                      ttCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGc                                                                                                                  >  1:446303/1‑140 (MQ=255)
                      ttCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCCCGCCGTTTCATGc                                                                                                                  >  2:342004/1‑140 (MQ=255)
                          gTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGa                                                                                                              <  1:1003238/140‑1 (MQ=255)
                          gTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGa                                                                                                              <  2:117712/140‑1 (MQ=255)
                          gTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGa                                                                                                              <  2:1039497/140‑1 (MQ=255)
                           tCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGAc                                                                                                             >  2:151150/1‑140 (MQ=255)
                            cTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTAAGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCCTGCCGGACt                                                                                                            >  2:503940/1‑140 (MQ=255)
                              gAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGGTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtga                                                                                                          >  1:951482/1‑140 (MQ=255)
                               aaaCTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtgat                                                                                                         >  1:822099/1‑140 (MQ=255)
                                aaCTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtgatg                                                                                                        >  2:135734/1‑140 (MQ=255)
                                aaCTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtgatg                                                                                                        >  1:363100/1‑140 (MQ=255)
                                aaCTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtgatg                                                                                                        >  1:914242/1‑140 (MQ=255)
                                  cTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtgatgat                                                                                                      <  2:209924/140‑1 (MQ=255)
                                  cTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACtgatgat                                                                                                      <  1:154760/140‑1 (MQ=255)
                                     ttCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTgatgatgat                                                                                                   >  2:294289/1‑140 (MQ=255)
                                     ttCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTgatgatgat                                                                                                   >  1:192649/1‑140 (MQ=255)
                                     ttCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTgatgatgat                                                                                                   >  1:928742/1‑140 (MQ=255)
                                          tACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGa                                                                                              <  1:817704/140‑1 (MQ=255)
                                               gTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTg                                                                                         >  1:736547/1‑140 (MQ=255)
                                                 aCCTTTTCGCTGGGCCTGGCGGGGAGGTTTGCCGGACGTGTTGGCAGTGGCATGTTGCCCTTTATGACCACGGGTTTCCTGCAAATTGGCCTCGGGTTCTCGCCGTTTTATGCCGGGCTGGTGATGTTCCCGATGGTGCt                                                                                       >  2:597841/1‑140 (MQ=255)
                                                    ttttCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTgg                                                                                    <  2:396090/140‑1 (MQ=255)
                                                     tttCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGgc                                                                                   <  2:699826/140‑1 (MQ=255)
                                                      ttCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCC‑TTATGACACCGGGTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGgcag                                                                                 >  2:371435/1‑140 (MQ=255)
                                                       tCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGgcag                                                                                 <  1:483781/140‑1 (MQ=255)
                                                       tCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGgcag                                                                                 <  1:552371/140‑1 (MQ=255)
                                                               ccTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGaa                                                                         >  1:407706/1‑140 (MQ=255)
                                                                cTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGGTTCTCGCCGGTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAAt                                                                        >  2:285994/1‑140 (MQ=255)
                                                                         aGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAAt                                                               <  2:497246/140‑1 (MQ=255)
                                                                          gCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAAtt                                                              <  1:763236/140‑1 (MQ=255)
                                                                           cTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATtg                                                             <  1:655306/140‑1 (MQ=255)
                                                                              tGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTgg                                                          <  1:294289/140‑1 (MQ=255)
                                                                                           ggCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGaa                                             <  1:135734/140‑1 (MQ=255)
                                                                                                tGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCt                                        <  2:298435/140‑1 (MQ=255)
                                                                                                tGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCt                                        >  1:685936/1‑140 (MQ=255)
                                                                                                tGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCt                                        >  2:872428/1‑140 (MQ=255)
                                                                                                  gCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGGCCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGAGAATCGCttt                                      >  1:835888/1‑140 (MQ=255)
                                                                                                   cATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTg                                     >  1:827215/1‑140 (MQ=255)
                                                                                                          cccTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTAtcg                              >  1:23233/1‑140 (MQ=255)
                                                                                                           ccTTTATGACACCGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTAtcgt                             <  1:483476/140‑1 (MQ=255)
                                                                                                                      ccGGTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGt                  <  1:335519/140‑1 (MQ=255)
                                                                                                                         gTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGc               >  1:882927/1‑140 (MQ=255)
                                                                                                                         gTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGc               >  1:657919/1‑140 (MQ=255)
                                                                                                                         gTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGc               >  1:390164/1‑140 (MQ=255)
                                                                                                                         gTTTTCCTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGc               >  2:834171/1‑140 (MQ=255)
                                                                                                                               cTGCAAATTGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGCGACCAc         >  2:584353/1‑140 (MQ=255)
                                                                                                                                      ttGTCCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGCGACCACGCTGGGt  <  2:192649/140‑1 (MQ=255)
                                                                                                                                      ttGACCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGCGACCACGCTGGGt  <  2:928742/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                        
CAGAAATAACAACCGTGCCCTGTTCAGTCTGAAACTGTTCCGTACTCGTACCTTTTCGCTGGGCCTGGCGGGGAGCTTTGCCGGACGTATTGGCAGTGGCATGTTGCCCTTTATGACACCGGTTTTCCTGCAAATTGGCCTCGGTTTCTCGCCGTTTCATGCCGGACTGATGATGATCCCGATGGTGCTTGGCAGCATGGGAATGAAGCGAATTGTGGTACAGGTGGTGAATCGCTTTGGTTATCGTCGGGTACTGGTAGCGACCACGCTGGGT  >  NC_000913/2162198‑2162471

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A