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 F108 I2 R1 19 69.6 2506112 90.8% 2275549 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,560,4551.G97.6% 118.9 / ‑5.3 42intergenic (‑2/+1)glpR/glpRpseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
Reads supporting (aligned to +/- strand):  ref base . (1/0);  major base G (23/17);  minor base A (0/1);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 4.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

GATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTG  >  NC_000913/3560316‑3560585
                                                                                                                                             |                                                                                                                                  
gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑cgca                                                                                                                                  >  1:265551/1‑140 (MQ=255)
                   ttGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGCACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGAGCAGGTGTTGCTCCGc                                                                                                               >  2:824940/1‑143 (MQ=255)
                               tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTCAg                                                                                                   >  1:1117963/1‑143 (MQ=255)
                               tCCGCCACGTGGCGGGCGAGGCGCTCTTTTTCTTCGGGCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                   <  1:225149/143‑1 (MQ=255)
                                    ccccttGCGGGCGGCGCGCGCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgc                                                                                              <  1:162282/139‑1 (MQ=255)
                                          gCGGGGGGTGCGGTCGTTTTCGTCGGGCGGGGGGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAGCTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgattacca                                                                                        <  2:774533/143‑8 (MQ=255)
                                                  tGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGTAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                                >  2:912587/1‑143 (MQ=255)
                                                     gcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGCTCGTGCCACGGCGTGTTAACCGAACTGGTAGGCCGCGCCGCTCCGTCATGATGC‑CGCAGGATCCGGTTTTGCTCCGCCATTCGATTGAGGGCGCGGCGAATAGTCCGCggg                                                                             >  2:893462/1‑143 (MQ=255)
                                                     gcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCCGGCGTGTTAACCGAACTGGAAGGCAGGGCCGCGCCGCCATGGTGG‑CGCAGGAGCAGGTTTTGCTGCGCCAGCTCAGTGGGGTGGCGGCGAATAGTCTGCggg                                                                             >  1:264027/1‑143 (MQ=255)
                                                     gcTCTTTTGCTGCGGGCTGGGTGGCCGTGGGATCGTGCCACGGCGTGTGAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTGTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCggg                                                                             <  2:464189/143‑1 (MQ=255)
                                                         tttttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGGCCCGCCAGCTCATTGAGGTCGCGGCGACTAGTCTGCGGGCTGa                                                                         >  2:550252/1‑143 (MQ=255)
                                                         tttttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTgg                                                                         >  1:933439/1‑142 (MQ=255)
                                                               ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGACGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTCTTGCTCCGCCAGCCCATTGCGGTCGCCGCGAATAGTCTGCCGGCCGACggcgg                                                                   >  2:506804/1‑140 (MQ=255)
                                                                         gTGGCCTGGCGATCGTGCCACGGCGTGTTAGCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTGATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                         <  2:1048982/143‑1 (MQ=255)
                                                                              cTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTCCCCGct                                                    >  1:546768/1‑143 (MQ=255)
                                                                              cTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTACGATAGGGTCGAAGAGTCCGCGGGCTGACGGAGAAATGCTCTACCAGct                                                    >  2:1212912/1‑143 (MQ=255)
                                                                               ttGCGATCGTGCCACGGCGTGTTCACCGAACTGGAAGGCAGCGCCGCACCGCCCTGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCAAATAGTCTGCGGGCTGACGGCGAAAGGCTCTACCAGccc                                                   >  2:349041/1‑141 (MQ=255)
                                                                               ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCGCTACGAGcgc                                                   >  2:344849/1‑141 (MQ=255)
                                                                                  cGATCGTGCCAGGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CACAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTc                                                <  2:60427/143‑1 (MQ=255)
                                                                                  cGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGAAGCGCCGCCCCGCCATGATGG‑CGGAGGACAAGGTCATGGTCCGCCAGCCAAGTGAGGTCGCGGCGAACAGTCTGCGGGCTCACGAAGAAATGATCTACCAGCTATTc                                                >  2:103119/1‑143 (MQ=255)
                                                                                    aTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                              >  2:482211/1‑143 (MQ=255)
                                                                                       gTGCGACGGCGTGTGAACCGCGCTGGAAGGCAGCGCCGCACCGCCAGGAGGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTAc                                           <  1:366788/143‑1 (MQ=255)
                                                                                       gTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTAc                                           <  1:995985/143‑1 (MQ=255)
                                                                                          ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGAG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCCCTACCAGCTCTTCCGTACTGa                                        >  1:1095570/1‑143 (MQ=255)
                                                                                           cACGGCGTTTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc                                       <  1:208276/143‑1 (MQ=255)
                                                                                           cACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGACATGCTCTACCAGCTCTTCGGTACGGAc                                       >  1:415729/1‑143 (MQ=255)
                                                                                           cACGGCGGGTTAGCCGAGCCGGAGGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc                                       <  2:106957/143‑1 (MQ=255)
                                                                                               gCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa                                   >  2:883236/1‑143 (MQ=255)
                                                                                                    ttAGCCGAGCTGGGTGGCAGCGCCGCACCGCCAGGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctg                              <  2:786700/143‑1 (MQ=255)
                                                                                                    ttAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAACctg                              >  1:536493/1‑143 (MQ=255)
                                                                                                      agccGAACTGTGAGGCAGCGCCGCACCGCCATGGTGG‑CGCAGGATCGGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                            <  2:757920/141‑1 (MQ=255)
                                                                                                       aCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgctg                           >  1:918535/1‑143 (MQ=255)
                                                                                                          gAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt                        >  2:709433/1‑143 (MQ=255)
                                                                                                          gAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGGCTGCGGGCTGACGGAGAAATGCTCTACTAGCTCTTCGGTACTGACATAACCCTGCTGttt                        <  1:492727/143‑1 (MQ=255)
                                                                                                            aCTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCTGCTCACACAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTaa                      <  1:912587/143‑1 (MQ=255)
                                                                                                             ctcgAAGGCCGCGCCGTATCGCCATGATGG‑CGCAGGAGCAGGTTTTGCTCCGCCAGCGCATTGAGGTCGCGGCGCATAGTCTGCGGGCTGACGGAGAAATGCTCTCCCAGCTCTGCGGTACTGACATAACCCTGCTGTTTAAc                     <  1:54193/140‑1 (MQ=255)
                                                                                                             cTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAc                     <  1:1238406/143‑1 (MQ=255)
                                                                                                                gAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGCGAAATGCTCTACCAGCTCTTCGGTACTGACCTAACCCTGCTGTTTACCCAg                  >  2:685450/1‑143 (MQ=255)
                                                                                                                  aGGCAGCGCCGCACTGTCATGATGG‑CGCAGGGTCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGACTAGTCGGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                <  2:16802/143‑1 (MQ=255)
                                                                                                                    gCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGCACTGACATACCCCTGCTGTTTAACCAGTTCg              >  2:1116225/1‑143 (MQ=255)
                                                                                                                     cAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa             <  1:618512/143‑1 (MQ=255)
                                                                                                                                cGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGAGGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCGGGTTAAGCAGTCCGATAACACAGtag  >  2:832680/1‑141 (MQ=255)
                                                                                                                                cGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAACCTGCTGCTTAACAAGCACGCTAATACCGTtg  >  2:604416/1‑143 (MQ=255)
                                                                                                                                             |                                                                                                                                  
GATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTG  >  NC_000913/3560316‑3560585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A