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 F63 I1 R1 5 63.7 3148838 93.9% 2956758 133.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947 1,648,882 +T intergenic (‑119/+177) oprB‑II ← / ← PP_1446 carbohydrate‑selective porin/TonB‑dependent receptor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,648,8811.T98.0% 158.7 / ‑4.2 50intergenic (‑118/+178)oprB‑II/PP_1446carbohydrate‑selective porin/TonB‑dependent receptor
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (25/24);  total (26/24)
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

GATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GA‑TATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCGG  >  NC_002947/1648734‑1649020
                                                                                                                                                     |                                                                                                                                           
gATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑Ga‑tt                                                                                                                                           >  2:346238/1‑149 (MQ=255)
    tAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑Ga‑ttatag                                                                                                                                       <  2:764078/150‑6 (MQ=255)
     aGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAgg                                                                                                                                       >  2:392717/1‑150 (MQ=255)
       cAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAgggg                                                                                                                                     >  1:1036420/1‑150 (MQ=255)
       cAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAgggg                                                                                                                                     >  2:1440916/1‑150 (MQ=255)
           ttttAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAATACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGGTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGt                                                                                                                                 >  1:1463756/1‑150 (MQ=255)
           ttttAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑Ga‑tta                                                                                                                                          >  2:904652/1‑138 (MQ=255)
           ttttAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑Ga‑tta                                                                                                                                          <  1:904652/140‑3 (MQ=255)
             ttAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTta                                                                                                                               <  1:392717/150‑1 (MQ=255)
              tAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTtat                                                                                                                              <  2:928182/150‑1 (MQ=255)
                     ttGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTAAAGGGGAAGTTATAAGaaaa                                                                                                                       >  2:71161/1‑150 (MQ=255)
                            aTGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACaa                                                                                                                <  1:128663/150‑1 (MQ=255)
                            aTGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACaa                                                                                                                >  2:1450950/1‑150 (MQ=255)
                                 aTAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGt                                                                                                           <  2:1017353/150‑1 (MQ=255)
                                 aTAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGt                                                                                                           >  1:1017353/1‑150 (MQ=255)
                                     cgcTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCg                                                                                                         >  2:218000/1‑148 (MQ=255)
                                     cgcTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCg                                                                                                         <  1:218000/148‑1 (MQ=255)
                                            ttttGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAgg                                                                                                                                       <  2:651672/111‑1 (MQ=255)
                                            ttttGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAgg                                                                                                                                       >  1:651672/1‑111 (MQ=255)
                                                gATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTc                                                                                                          >  1:233072/1‑136 (MQ=255)
                                                gATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTc                                                                                                          <  2:233072/136‑1 (MQ=255)
                                                 attattGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTAAAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttgt                                                                                           <  1:71161/150‑1 (MQ=255)
                                                  ttattaAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttgtt                                                                                          <  2:1079328/150‑1 (MQ=255)
                                                  ttattGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttgtt                                                                                          >  2:1352999/1‑150 (MQ=255)
                                                     ttGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGaa                                                                                       >  2:811615/1‑150 (MQ=255)
                                                         aaaaaaCGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACggg                                                                                   <  2:1569774/150‑1 (MQ=255)
                                                                 gCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAgtc                                                                           >  1:563215/1‑150 (MQ=255)
                                                                   aaGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgtt                                                                                             >  2:1320309/1‑130 (MQ=255)
                                                                   aaGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgtt                                                                                             <  1:1320309/130‑1 (MQ=255)
                                                                     gcgcATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCa                                                                       >  1:422623/1‑150 (MQ=255)
                                                                     gcgcATCGAAGGGCGGGCCCCTCAAGGGATATGGCGACAAGATTGTTCGATGAAGCGTTGTAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCa                                                                       <  1:1197667/150‑1 (MQ=255)
                                                                      cgcATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGGAGATGTGAG‑TATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCAt                                                                      <  1:1450950/150‑1 (MQ=255)
                                                                             aaGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGa                                                               <  2:422623/150‑1 (MQ=255)
                                                                             aaGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGa                                                               >  1:209124/1‑150 (MQ=255)
                                                                              aGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAg                                                              <  2:209124/150‑1 (MQ=255)
                                                                               gggcgggcCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAgg                                                             <  1:1352999/150‑1 (MQ=255)
                                                                                  cgggcCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAg                                                          <  2:993099/150‑1 (MQ=255)
                                                                                    ggcCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAgat                                                        >  2:1421256/1‑148 (MQ=255)
                                                                                     gcCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACaa                                                                                                                <  2:575292/93‑1 (MQ=255)
                                                                                     gcCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACaa                                                                                                                >  1:575292/1‑93 (MQ=255)
                                                                                         cTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGaaaaaa                                                                                                                     <  1:1239580/84‑1 (MQ=255)
                                                                                         cTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGaaaaaa                                                                                                                     >  2:1239580/1‑84 (MQ=255)
                                                                                         cTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAgg                                                   >  2:1172625/1‑150 (MQ=255)
                                                                                          tCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGggag‑ga                                                                                                                                              >  2:533414/1‑58 (MQ=255)
                                                                                          tCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGggag‑ga                                                                                                                                              <  1:533414/58‑1 (MQ=255)
                                                                                             aTGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCg                                               >  1:5593/1‑150 (MQ=255)
                                                                                               ggATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCggg                                             <  1:1421256/150‑1 (MQ=255)
                                                                                               ggATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAAGGGAAGTAGTCAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCggg                                             <  1:811615/150‑1 (MQ=255)
                                                                                                 atatGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGtt                                           >  2:459468/1‑150 (MQ=255)
                                                                                                           aaGCTTGTTCGATGAAGCGTTTCAGGTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGaa                                 <  2:1269249/150‑1 (MQ=255)
                                                                                                                     gATGAAGCGTTTCAGCTTGCGGCGGGGAGAAA‑TATAGGGGAAGTTATAAGAAAAAAGACAAATTTTCGCAGAGGATTGTAGTTGAACGGGCAACACTCCTCATTAATCGAGGCAAGTGTAGAAGAGGGTTAACCAGCAAAAGCGcccatt                       >  2:148894/1‑146 (MQ=255)
                                                                                                                        gAAGCGTTTCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGcc                    >  2:1425276/1‑150 (MQ=255)
                                                                                                                               ttCAGCTTGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCAt             >  2:682402/1‑150 (MQ=255)
                                                                                                                                     ttGCGGCGGGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACAATCGTAtt       >  2:1318820/1‑150 (MQ=255)
                                                                                                                                         ggcggGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTcgcg   <  2:774721/150‑1 (MQ=255)
                                                                                                                                          gcggGGAG‑GATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCgg  <  1:1172625/150‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                           
GATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAG‑GA‑TATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCGG  >  NC_002947/1648734‑1649020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A