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 F91 I0 R1 918 53.4 2573728 94.2% 2424451 136.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,842,949:1 +G 22.8% intergenic (+48/‑249) ccoP‑II → / → PP_4259 cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,842,9491.G22.8% 149.2 / 55.5 57intergenic (+48/‑249)ccoP‑II/PP_4259cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
Reads supporting (aligned to +/- strand):  ref base . (25/19);  new base G (7/6);  total (32/25)
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

CGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCATACTGC  >  NC_002947/4842804‑4843095
                                                                                                                                                  |                                                                                                                                                  
cGGCACAGGCACAACAGCGGGGGAGCTACGATGTGCACTTGCGGGCGGCTTATGTCTACAGCCTGTCGGACCAGGCTGAGTCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTa                                                                                                                                                <  2:1037584/150‑1 (MQ=37)
   cccAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGa                                                                                                                                             <  2:491594/150‑1 (MQ=255)
        gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCggg                                                                                                                                        <  1:1224052/150‑1 (MQ=255)
               tGCAGGGCAACGACAAGGTGTACTTGCTGGCGGCTTACATCTACAGCCTGTAGCAGCAGGATGAGCCGCGCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACACGCTCCTACAAAGGCTACT‑TGTAGAGGAGGGCTTAccc                                                                                                                                 >  2:88765/1‑150 (MQ=255)
               tGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTAccc                                                                                                                                 >  1:548127/1‑150 (MQ=255)
                  aGGGCAACGACAAGGTGCACTTGCTTGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCcgcg                                                                                                                              >  1:784459/1‑150 (MQ=255)
                      cAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCgg                                                                                                                                         >  2:298356/1‑135 (MQ=255)
                      cAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCgg                                                                                                                                         <  1:298356/135‑1 (MQ=255)
                       aaCGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAagag                                                                                                                         <  2:824304/150‑1 (MQ=255)
                        aCGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAgg                                                                                                                        <  2:548127/150‑1 (MQ=255)
                            cAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCgg                                                                                                                    >  2:338527/1‑150 (MQ=255)
                                            gcggcTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGc                                                                                                                                           <  1:297062/111‑1 (MQ=255)
                                            gcggcTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGc                                                                                                                                           >  2:297062/1‑111 (MQ=255)
                                                       cTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCaa                                                                                         <  2:784459/150‑1 (MQ=255)
                                                               tGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTg                                                                                 >  2:393182/1‑150 (MQ=255)
                                                                   gCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGGCTCTTCGCGGGTGCACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGAATTTCTCGCAGGCAAGTGACCTGGATc                                                                             >  1:548416/1‑150 (MQ=255)
                                                                   gCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATc                                                                             >  1:374688/1‑150 (MQ=255)
                                                                    cACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACt                                                                                                                >  1:1114053/1‑114 (MQ=255)
                                                                    cACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACt                                                                                                                <  2:1114053/114‑1 (MQ=255)
                                                                     aCCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAg                                                                                                                                               >  1:264959/1‑82 (MQ=21)
                                                                     aCCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAg                                                                                                                                               <  2:264959/82‑1 (MQ=21)
                                                                       cAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGc                                                                                               >  2:47871/1‑128 (MQ=255)
                                                                       cAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGc                                                                                               <  1:47871/128‑1 (MQ=255)
                                                                              aGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACAccc                                                                  <  2:374688/150‑1 (MQ=255)
                                                                               gCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCg                                                                 <  1:338527/150‑1 (MQ=255)
                                                                                  ggCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAt                                                                          >  2:365383/1‑138 (MQ=255)
                                                                                  ggCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAt                                                                          <  1:365383/138‑1 (MQ=255)
                                                                                    ccAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTAccc                                                                                                                                 <  2:840551/81‑1 (MQ=255)
                                                                                    ccAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTAccc                                                                                                                                 >  1:840551/1‑81 (MQ=255)
                                                                                      aaGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGt                                                                                                                                                 <  1:684318/63‑1 (MQ=255)
                                                                                      aaGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGt                                                                                                                                                 >  2:684318/1‑63 (MQ=255)
                                                                                                         ctggcctCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAAcc                                       >  1:1100778/1‑150 (MQ=255)
                                                                                                             cctCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAAc                                   >  2:1151666/1‑150 (MQ=255)
                                                                                                                 ttCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGa                               <  1:526092/150‑1 (MQ=255)
                                                                                                                     cgGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAAc                                        <  2:174351/137‑1 (MQ=255)
                                                                                                                     cgGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAAc                                        >  1:174351/1‑137 (MQ=255)
                                                                                                                      gggTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTaaa                          >  2:544908/1‑150 (MQ=255)
                                                                                                                            aCCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGc                    >  2:849364/1‑150 (MQ=255)
                                                                                                                             cccGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCa                   >  2:84574/1‑150 (MQ=255)
                                                                                                                             cccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCGTTTCTCGCAg                                                                                             <  2:222445/76‑1 (MQ=14)
                                                                                                                             cccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCGTTTCTCGCAg                                                                                             >  1:222445/1‑76 (MQ=14)
                                                                                                                             cccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCACCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCa                   >  2:391722/1‑150 (MQ=255)
                                                                                                                              ccGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAAc                                        >  2:1010606/1‑128 (MQ=255)
                                                                                                                              ccGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAAc                                        <  1:1010606/128‑1 (MQ=255)
                                                                                                                              ccGCTCCTACACAGGATCCT‑TGTAAGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATAGCACGAACCCAACGCGACTACAGGTCGCAg                  >  1:522321/1‑150 (MQ=255)
                                                                                                                              ccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCa                                                                                              <  2:1103120/74‑1 (MQ=17)
                                                                                                                              ccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCa                                                                                              >  1:1103120/1‑74 (MQ=17)
                                                                                                                               cGCTCCTACACAGGATCCA‑TGTAGGAGCCGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGCCCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGt                 <  2:522321/150‑1 (MQ=255)
                                                                                                                                gCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTg                >  1:1024338/1‑150 (MQ=255)
                                                                                                                                  tCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAtt                                                                         >  1:898531/1‑91 (MQ=255)
                                                                                                                                  tCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAtt                                                                         <  2:898531/91‑1 (MQ=255)
                                                                                                                                    cTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGaa            <  1:849364/150‑1 (MQ=255)
                                                                                                                                      acacAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGGCTAAAGGTCGCAGTGCGAAcc          >  2:659167/1‑150 (MQ=255)
                                                                                                                                       acaaGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAAcc          >  2:884545/4‑150 (MQ=255)
                                                                                                                                         aaGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAacac                                                        >  2:212483/2‑102 (MQ=255)
                                                                                                                                         aaGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAacac                                                        <  1:212483/101‑1 (MQ=255)
                                                                                                                                              tCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCATACTGc  >  1:1066158/1‑150 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
CGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCATACTGC  >  NC_002947/4842804‑4843095

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

GATK/CNVnator alignment

N/A