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 F17 I0 R1 155 84.1 1797446 90.9% 1633878 230.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 743,686 C→G 34.3% R32G (CGA→GGA)  ybgJ → putative allophanate hydrolase, subunit 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913743,6860CG34.3% 28.8 / 4.0 29R32G (CGA→GGA) ybgJputative allophanate hydrolase, subunit 1
Reads supporting (aligned to +/- strand):  ref base C (15/3);  new base G (8/2);  total (24/5)
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

TGCTGCAGGTCACCATGCCACTGAACGTGGTGGTATTCGCGCATTGAGCGAGTGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGTGGTTTACGGTGGTGCAGGCGGACCGGATTTGGCGGTGGTCGCGGCGCAT  >  NC_000913/743459‑743916
                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                        
tgctgcAGGTCACCATGCCACTGAACGTGGTGGTATTCGCGCATTGAGCGAGTGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGAAGTGCTGGG‑ACTGGAACCGCCGGGGACGCTGGACAGCCAGAAACGGA‑TGTGGGGACTTgcggcg                                                                                                                                                                                                                               >  2:875990/1‑236 (MQ=255)
  ctgcAGGTCACCATGCCACTGAACGTGGTGGTATTCGCGCATTGAGCGAGTGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGCAGCGCTTGA‑ACTGGAACAGCCGGTGACGCGGGCTAACCAAGAACCGA‑TCTGGCggcgagcgccacg                                                                                                                                                                                                                             >  2:661841/1‑227 (MQ=255)
     cAGGTCACCATGCCACTGAACGTGGTGGTATTCGCGCATTGAGCGAGTGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGG‑ACTGGAACCCCCGGTGACGCTGGCTAGCCAGAAACGGA‑GCTGGGGACTgggccgcgggcc                                                                                                                                                                                                                          >  2:239081/1‑229 (MQ=255)
     cAGGTCACCATGCCACTGAACGTGGTGGTATTCGCGCATTGAGCGAGTGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGGGCTGGA‑ACTGGAACCCCCGGTGCCGCGGGCTAGCCCGAAACGGA‑TCTGGGGACTGgcgccgggccc                                                                                                                                                                                                                          >  2:295174/1‑232 (MQ=255)
                  cACTGAACGTGGTGGTATTCGCGCATTGAGCGAGCGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGGGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGGGCTGGACAGTGGAAGC‑CCGGTGACGCTGGCTAGCCGGAAACAGA‑CCTGGGGCCGGGCGCAACgccggggggggaggcgg                                                                                                                                                                                                             >  1:490127/1‑223 (MQ=255)
                                                                aaTACCGATCTTGATGAGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGACAGGCTGGG‑ACTGGAACCCCCCGGGACGATGGCAAGCCAGAAACGGACTATGG‑GGCTGGCGCACCGTCCGGTGGTGAGTCCCGCA‑GAGGTGGAAGCCCTTCCCGGCAGGAAAAATAACaacgagagtt                                                                                                                                                              >  1:389246/1‑230 (MQ=255)
                                                                            gATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGGGGGTA‑TGCCGCATGGGGTTGAAGCCATTCCCGGCATGAACAATATcttgctcttttacacatctccg                                                                                                                                                   >  2:744383/1‑217 (MQ=255)
                                                                                  aCCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGG‑ACTGGAACCGCCGGGGACGCTGGCTAGCCAGAAACGGA‑TCTGGGGACTGGCGCAGCGTCTGGTGGATA‑TGCCGCATTTGGTTGAAGGCATTTCCGGCAGGAAAAATATCACGGGGGTTTTGCGGAAACCttgtgcgc                                                                                                                                            >  2:793426/1‑232 (MQ=255)
                                                                                  aCCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTTGCCAGAAACGGA‑TCTGGCGACTGGCGCCGCGGCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATACCGGGGATTTTGCGTAATCCTTAGT‑cgc                                                                                                                                           >  2:453715/1‑239 (MQ=255)
                                                                                  aCCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGAAGCTTGCTAGCCAGAAACGGA‑TCTGGGGACTGGCGCAGCGGCTGGTGGATA‑TGCCGAATTTGGTTGAAGCCATTCCCGGCATGACAAATATTACGGTGGTTTTGCGTAATCCTGAGT‑c                                                                                                                                             >  2:847480/1‑237 (MQ=255)
                                                                                  aCCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGAATTGCTGTG‑AATGGAACCGCCGGTGACGCGGGCTAGCCAGACAAGGG‑TGTGGCGACCGGGGCCGCGGCCGGTGGGAA‑TTCCGAATAGGGTTGAAGCCAATCCCGGCATGAACCATTATACGGCGGTTTTTCGGAATACTAGGT‑cgc                                                                                                                                           >  1:526916/1‑239 (MQ=255)
                                                                                            atatTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGGGACGCTGGCTAGCCAGAAAAGGA‑TCTGGCGACTGGCGCCGCGTCTGGTGGGTA‑TGCCGAAATTGGTTGAAGCCATTCCCGGCATGAAAAAAATCACGGGGGTTTTGCGGAATCCGGAggtcccggggccggg                                                                                                                                  >  2:238483/1‑225 (MQ=255)
                                                                                               ttCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGGCTGGCGCAGCGGCTGGTGGGTA‑TTCCGAATGTGGTTTAAGGCATTCCCGGCATGGACAATATCACGGGGATTTTGCGGAATCCTAGGT‑cgcttggctcgggtg                                                                                                                               >  2:27711/1‑227 (MQ=255)
                                                                                                           cATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGG‑ACTGGAACCGCCGGTGACGCCGGCTAGCCAGAAACAGG‑ACTGGGGCCCGGCGCAGCGGCTGGTGGATA‑TTCCGCATGTGGTTGGAGGCATTCCCGGCATGAACAAAATCACGGGGATTTTTCGTAAACCTGGGTGCACGGGC‑CGGGATGCCATagagaggtt                                                                                                                  >  1:57622/1‑234 (MQ=255)
                                                                                                           cATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGG‑AAAGGAACCGCCGGTGACCCTGGCCAGCCCGGAACGGG‑TCAGGGGACTGGCGGCGCCGCCGGGGGATA‑TGCCGCAAGGGGTTGGAGCCCTTCCCGCCCTGGCAAATATCACAGGGCTTTTTGGTAACCCTCGGT‑cgcggggcgcggagtacaacaagagttt                                                                                                                  >  1:409753/1‑217 (MQ=255)
                                                                                                           cATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAACCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGGGATTTTGCGTAATCCTGAGG‑CCCTGGCGCTGGATGCCCTAGAGGGttt                                                                                                                  >  2:541094/1‑239 (MQ=255)
                                                                                                            aTAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGGGACGCTGGCTACCCAGAAACGGG‑TCTGGCGGCTTGCGCCGCGTCTGGTGGGTA‑TGCCGAAAGTGGGTTAAGCCCTTCCCGGCATTAAAAATATCACCGGGGTTTTTCGTAATCCTCAGT‑CGCTGGGGCTGGGTGcccaaaaggggttg                                                                                                                 >  1:713151/1‑227 (MQ=255)
                                                                                                                                                                 ggTGAAACGGCGGAAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGCATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGGGTAATCCTGAGG‑CGCTGGCGCTGGATGCCCTAGAGCGCTTTCTACACTGCTGGGGGGGGGCCGAGGCGCGGGAGCCGGAgggtcggtgtctgta                                                            >  1:784394/1‑225 (MQ=255)
                                                                                                                                                                       aCGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCCAGCCAGAAAAGGA‑TCTGGCGGCTGGCGCCGCGTCTGGGGGATA‑TGCCGGAAGTGGTTGAAACCCTTCCCGGCCTGGACAAAAATACGGTGGTTTTGGTTAATACTGCGG‑CGCTGGGGCGTGGTTCCATAGAGCGTTTGAGACGCTGGGGGGGGGAGGAGGGGGGGGGGGGGCCGCGGTCTCGCTTTATTTaaaagtc                                                      >  1:517608/1‑235 (MQ=255)
                                                                                                                                                                          ggtggaggtgcgggagtgtgacccgccgGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCgg                                                    <  2:558643/217‑1 (MQ=255)
                                                                                                                                                                           ggggtaggggagaaaggcgcacCGCCGGTGACGGTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGGCGAATGTTGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCgg                                                    <  2:466757/218‑1 (MQ=255)
                                                                                                                                                                             gTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGAGTTTGCAACGCTGGGGGGAGGCGAGCGGGGCGCGGGAGCCGGAGTCTCGCTTTTTTGAAATTCCgggggt                                                >  2:801144/1‑239 (MQ=255)
                                                                                                                                                                                     tatgagagtccccgccgGTGACTGTGGCTGGCGAGAAACGGA‑TTTGGGCATTGGGGGAGCGTCTGGTGGATT‑GGCCGAATGTGGTTGAAGCCAATCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGGTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGTGGTTTACgg                                          <  1:875990/227‑1 (MQ=255)
                                                                                                                                                                                         actggaacCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCCGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGACCAATATCACGGTGATTTTGCGTAATCCTGAGC‑CGCTGGCGCTGGAGGCCATCGAGCGTTTGCAACGCTGGTGGGTGGAGAGCGAGGGGCTGGAGCCGGAGTCCCGCTTTCTTGAAATCCCGGGGGtttcaggaggg                                      >  1:161457/1‑230 (MQ=255)
                                                                                                                                                                                                 cgccgGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGCGAGCGAGGCGCTGGGGCCGGAGTCTCCCTTTATTACAATTCCGGTGGGTTCTGGTGGTGCAGGCgg                              >  2:367581/1‑238 (MQ=255)
                                                                                                                                                                                                   ccgGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGGGGTTTACGGTGGTGCAGGCGGAcc                           >  2:492820/1‑239 (MQ=255)
                                                                                                                                                                                                            cTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGCAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGGGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGAGGGTTACGGGGGGGCAGGCGGACCGGATTTGGc                  >  2:97899/1‑239 (MQ=255)
                                                                                                                                                                                                              ggcgaggcaagaaCGGT‑TTTGGGGACGGGGGCAGGGGTGGGTGGATA‑TGTCGAATGTGGTTGAAGCCATTCCCGGCATGAACAAGATCACGGTGAGTTGGCGTAATCCTGAGG‑CGCTGGCGCTGGATGCCAGAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGTGGTTTACGGTGGTGCAGGCGGACCGGATTTGGCg                 <  1:367581/227‑1 (MQ=255)
                                                                                                                                                                                                                            ggA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGGTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGTGGTTTACGGTGGTGCAGGCGGACCGGATTTGGCGGTGGTCGCGGCGCAt  <  2:80368/239‑1 (MQ=255)
                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                        
TGCTGCAGGTCACCATGCCACTGAACGTGGTGGTATTCGCGCATTGAGCGAGTGGCTGAATGAAAATACCGATCTTGATGTGACCTTTATTGATATTCCTAATCCTGCATAACGAATAATCAGAGGGATCGAAAGTGCAACGAGCGCGTTGTTATCTGATAGGTGAAACGGCGGTAGTGCTGGA‑ACTGGAACCGCCGGTGACGCTGGCTAGCCAGAAACGGA‑TCTGGCGACTGGCGCAGCGTCTGGTGGATA‑TGCCGAATGTGGTTGAAGCCATTCCCGGCATGAACAATATCACGGTGATTTTGCGTAATCCTGAGT‑CGCTGGCGCTGGATGCCATAGAGCGTTTGCAACGCTGGTGGGAGGAGAGCGAGGCGCTGGAGCCGGAGTCTCGCTTTATTGAAATTCCGGTGGTTTACGGTGGTGCAGGCGGACCGGATTTGGCGGTGGTCGCGGCGCAT  >  NC_000913/743459‑743916

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A