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
A1 F1 I1 R1 154 26.6 2069536 90.2% 1866721 108.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 1,191,426 Δ1 bp coding (350/390 nt) h16_A1095 ← Hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604791,191,4240G.100.0% 21.1 / NA 6coding (352/390 nt)h16_A1095Hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (3/3);  total (3/3)

CAGCGGCCGGGGCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCCGGGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCG  >  AM260479/1191333‑1191488
                                                                                           |                                                                
cAGCGGCCGGGGCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGccac                       >  2:582345/1‑134 (MQ=255)
          ggCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCcgcg             <  1:582345/134‑1 (MQ=255)
                                                                                  ggtCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCgcgcgcggcg  <  1:191626/73‑1 (MQ=255)
                                                                                  ggtCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCgcgcgcggcg  >  2:191626/1‑73 (MQ=255)
                                                                                    tCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCgcgcgcggcg  <  1:918905/71‑1 (MQ=255)
                                                                                    tCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCgcgcgcggcg  >  2:918905/1‑71 (MQ=255)
                                                                                           |                                                                
CAGCGGCCGGGGCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCCGGGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCG  >  AM260479/1191333‑1191488

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGGCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCCGGGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCGCGCGCTGCCATGGATTGCGTTGCGGTCCCTGTGGCCCGTGGTGTTGCCGCCTCAGCTGCCTGTGCCTGCAGCCACGCGCTGGCA  >  AM260479/1191342‑1191572
                                                                                    |                                                                                                                                                  
GGGCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCGCGCG                                                                                  <  GWNJ‑0478:712:GW2002102894th:2:2104:4592:52416/150‑1 (MQ=60)
           gagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCAGCACGATGCTGGTGGTCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCGCGCACTGCCATGGAT                                                                       <  GWNJ‑0478:712:GW2002102894th:2:1112:13802:30783/104‑1 (MQ=60)
           acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCACGATGCTGGTGGTCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCGCGCGCTGCCATGGAT                                                                       <  GWNJ‑0478:712:GW2002102894th:2:2211:14255:50277/101‑1 (MQ=60)
                                                                 ATGCTGGTGGTCAGCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCGCGCGCTGCCATGGATTGCGTTGCGGTCCCTGTGGCCCGTGGTGTTGCCGCCTCAGCTGCCagcgcgtgg                 >  GWNJ‑0478:712:GW2002102894th:2:1201:12588:49630/1‑141 (MQ=60)
                                                                              GCCC‑GGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGC‑‑CGCGCGCGCGGCGCGCGCTGCCATGGATTGCGTTGCGGTCCCTGTGGCCCtgtctcatatacacatctccgagcccacgggacggagctacatctcg  >  GWNJ‑0478:712:GW2002102894th:2:2214:4105:54033/1‑103 (MQ=60)
                                                                                    |                                                                                                                                                  
GGGCGGACACCTGTTCAGGCGCCGACGCCGGCAGCAGTGCGCCATCATCGATCTGCCGCAGCACGATGCTGGTGGTCAGCCCGGGCCACTGCCGCGACGCTGGCCACTAGCCCGAGCGAGCGCCACCACCGCCGCGCGCGCGCGGCGCGCGCTGCCATGGATTGCGTTGCGGTCCCTGTGGCCCGTGGTGTTGCCGCCTCAGCTGCCTGTGCCTGCAGCCACGCGCTGGCA  >  AM260479/1191342‑1191572

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑