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
A3 F28 I0 R1 51 55.9 1320120 86.3% 1139263 218.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,355,507 G→C 20.3% P261P (CCG→CCC)  gltB → glutamate synthase, large subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,355,5070GC20.3% 51.9 / 2.8 37P261P (CCG→CCC) gltBglutamate synthase, large subunit
Reads supporting (aligned to +/- strand):  ref base G (23/6);  new base C (5/3);  total (28/9)
Fisher's exact test for biased strand distribution p-value = 3.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.44e-01

CTGTGTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCATGCATATGGAGCCGTGGGATGGCCCGGC  >  NC_000913/3355289‑3355734
                                                                                                                                                                                                                          |                                                                                                                                                                                                                                    
cTGTGTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCCATGGGCGCGCGCGCGTACTTATAAATTCCAGACACCGCTTATccc                                                                                                                                                                                                                              >  1:4869/1‑227 (MQ=255)
cTGTGTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCCCGTACTTATAAATTCCAGACACCCCTTATCCCt                                                                                                                                                                                                                             >  2:56449/1‑228 (MQ=255)
 tgtgTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTTTTCCACCAGCGCTTCTCCACTCACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGGAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAAACACCCGTTAACCCt                                                                                                                                                                                                                             >  2:532745/1‑227 (MQ=255)
 tgtgTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTTGCGCATACCGGTGAAATCAACACCACCACCGGTAACCGCCAATGGGCGCGTGCCGGGAGTTATAAATTCCAGACACCCCTTATCCCt                                                                                                                                                                                                                             >  1:267184/1‑227 (MQ=255)
 tgtgTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTAATCCCt                                                                                                                                                                                                                             >  1:470015/1‑227 (MQ=255)
 tgtgTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGCACTTATAAATTCCAAACACCCCTTATCCCt                                                                                                                                                                                                                             >  2:105548/1‑227 (MQ=255)
             cGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGTCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCCCGTACTTATAAATTCCAGACACCGCTTAGCCCTGACCTGCccgacg                                                                                                                                                                                                                >  1:259750/1‑228 (MQ=255)
             cGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTTCacgact                                                                                                                                                                                                                >  1:372390/1‑227 (MQ=255)
                                         tGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATAAACACCATAACCGGTAACAGCCAATGGGCGCGGGCGCGTACTTATAAATTCCAGACACGGCTTATCCCTGACCTGCACCACGCCGCACCGTTCGTCAACGAAACCGGct                                                                                                                                                                                     >  1:176362/1‑227 (MQ=255)
                                                     tCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGc                                                                                                                                                                                                                      >  1:299447/1‑182 (MQ=255)
                                                                                   gcgcTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCACCGAAACCGGCCCTGACTCCAGTTCGATGGATAACATCTGGGAACTGCTGCTGGc                                                                                                                                          >  2:618547/1‑228 (MQ=255)
                                                                                                 acacCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACCAAACCGGCTCTGACTCCCGTTCGATGGATAACTTGCTGGAACTGCTGCTGCCAGGCgggcaggaaa                                                                                                                            >  2:153818/1‑221 (MQ=255)
                                                                                                     cGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCCGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCCggatggaaaacaa                                                                                                                        >  2:23416/1‑222 (MQ=255)
                                                                                                      gTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCACCGAAACCGGCCCTGACCCCAGTTCGATGGATAACATCCTCGAACTGCGTCTCGCAGGCGGGATGGataatatc                                                                                                                       >  2:159356/1‑223 (MQ=255)
                                                                                                      gTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATatcatc                                                                                                                       >  1:462416/1‑228 (MQ=255)
                                                                                                      gTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCCCTTATCCCTGCCCTGCACGACGCCGAACCGTCCGTCACCGAAACCGGCCCTGACACCAGTTCGATGGTTAACATCCTGGAACGCCCGCCGGCAGGCGggacggagacacac                                                                                                                       >  2:92121/1‑221 (MQ=255)
                                                                                                        aCCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCCCTGCATCCAGTTCGATGGATAACAGGCTGGAAATGCTCCTGTCAGCCGggatggtaatcctc                                                                                                                       >  1:268000/1‑218 (MQ=255)
                                                                                                           gcgcTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGCCTCCAGTTCGATGGATAACATGCTGGACCTGCTGCTGCCAGGCGGGATGGATCTCATCCgcgc                                                                                                                  >  1:13910/1‑228 (MQ=255)
                                                                                                            cgctggccgctggcGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGCTGGCTCACATGCTGGAACTGCTGCTGGCAGGCGGGATGGAGTTCATccccccc                                                                                                                 >  1:380210/1‑223 (MQ=255)
                                                                                                            cgctggccgctggcGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACCCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGCTAACATGCTGGAACTGCTGGTGGCAGGCGGGGAGGGAATCATCCGCGcc                                                                                                                 >  2:657628/1‑228 (MQ=255)
                                                                                                                                gTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGACAACATGCTGGAACTGCTGCTGCCAGCCGGGATGGATATAATCCGCGCCATGCGTCTATTAGTac‑cacc                                                                                            >  1:234506/1‑228 (MQ=255)
                                                                                                                                   cctctcgcgggCCCATGACGGAAAAAACCACCCCATCCCCGGAACCCGCCAATGGGCCCGTGCGCGTTCTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCg                                                                                          <  1:92121/218‑1 (MQ=255)
                                                                                                                                              cgcATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCCCTGACTCCAGTTCGATGGATACCATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCTTCCCGCCCCTGGGTCTTTTAGTAC‑CACCCGCCCGCCAGaaca                                                                              >  2:364543/1‑228 (MQ=255)
                                                                                                                                                   aaCGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGCAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGACCTGCTGCTGCCAGGCGGGATGGTTATCATCCGCGCCATGCGTCTCTTATTAC‑CACCCGCCTTGCATAACATCCCg                                                                         >  1:585319/1‑228 (MQ=255)
                                                                                                                                                   aaCGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGCTGGCTAACATGCTGGAACTGCTGCTGGCATGCGGGATGGAAATCATCCGCGCCACGCGTCCTTTATAAC‑CACCCCCCTGGCAGAAAAACCCg                                                                         >  2:513604/1‑228 (MQ=255)
                                                                                                                                                        tGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGCTAACATGCTGGAACTGCTGCTGGCAGGCGGGAGGGGTATCATCCCCGCCATGCGGCTATTAGTAC‑CCCCCGCCTGGCAGACCAACCCgagtag                                                                    >  2:155220/1‑223 (MQ=255)
                                                                                                                                                                  acCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTCCTTATAACTTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCCCCGACTCCAGTTCGACGGCTAACATGCTGGAACTCCTGCTGGCAGACGGGATGGTTAACAGCCGCGCCATGCGCCTATTACTACACACGCCCGTGGC‑GAACAACCCGGGAATGGACCCggg                                                           >  2:26400/1‑226 (MQ=255)
                                                                                                                                                                                 cGCCAGTGGGCGGGTGCGCGTACTTATAAATCCCAGACACCGCTTACCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAGACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATAGCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCttt                                           <  2:253230/228‑1 (MQ=255)
                                                                                                                                                                                 cGCCAATGGGCGCGTGCCCGGACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCttt                                           <  1:23416/228‑1 (MQ=255)
                                                                                                                                                                                 cGCCAATGGGCGCGTGCACGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCttt                                           <  1:56449/228‑1 (MQ=255)
                                                                                                                                                                                         ggcccttgcgcgtGTTTTGAAATTCCAGACACCCCTTCTCCCGGTCCTGCACGACGCCGCTCCGGTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTCTTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTaa                                   <  2:267184/222‑1 (MQ=255)
                                                                                                                                                                                               tggggttACTTAAAAATTCCAAACCCCCCTTACCCCTGGCCTGCACGAGGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCAt                             <  2:462416/222‑1 (MQ=255)
                                                                                                                                                                                               tgcgcgtACTTATAAATTCCAGACCCCCCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCAt                             <  1:465544/228‑1 (MQ=255)
                                                                                                                                                                                               ggcgcatACTTAAAAATTCCAGTCACCGCTGATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCAt                             <  1:153818/227‑1 (MQ=255)
                                                                                                                                                                                                       cTTATAAATTCCAGACACCGCTTACCCCTGGCCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCATGCATATg                      <  1:136726/227‑1 (MQ=255)
                                                                                                                                                                                                                    gACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGCCTATTAGTAC‑CACCCCCCTGTCAGAACAACCCGGATATGGGACCGGAACTGCGTGCCTTCTTTGACTTTACCTCCATGCCTATGGCGCCGTgggtggg        >  2:502554/1‑224 (MQ=255)
                                                                                                                                                                                                                       acCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTATTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGGGCCTCCTTTGCCTTTAACTCCAGCCATATGAATCCGTGGGAGTGccc     >  1:551090/1‑228 (MQ=255)
                                                                                                                                                                                                                          gCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCATGCATATGGAGCCGTGGGATGGCCcggc  >  1:118540/1‑228 (MQ=255)
                                                                                                                                                                                                                          |                                                                                                                                                                                                                                    
CTGTGTATGCCGACGGATCTGCCGCGCTTTTATCTGGATCTTGCGGACCTGCGTCTGGAATCGGCCATTTGCCTGTTCCACCAGCGCTTCTCCACTAACACCGTACCGCGCTGGCCGCTGGCGCAACCGTTCCGCTATCTGGCGCATAACGGTGAAATCAACACCATCACCGGTAACCGCCAATGGGCGCGTGCGCGTACTTATAAATTCCAGACACCGCTTATCCCTGACCTGCACGACGCCGCACCGTTCGTCAACGAAACCGGCTCTGACTCCAGTTCGATGGATAACATGCTGGAACTGCTGCTGGCAGGCGGGATGGATATCATCCGCGCCATGCGTCTATTAGTAC‑CACCCGCCTGGCAGAACAACCCGGATATGGACCCGGAACTGCGTGCCTTCTTTGACTTTAACTCCATGCATATGGAGCCGTGGGATGGCCCGGC  >  NC_000913/3355289‑3355734

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A