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
MC JC AM260479 1,464,441 Δ37 bp coding (125‑161/552 nt) h16_A1354 → conserved hypothetical protein

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ AM260479 1464441 1464477 37 26 [0] [0] 28 h16_A1354 conserved hypothetical protein

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AM260479 = 14644400 (0.000)26 (0.990) 23/216 0.2 100% coding (124/552 nt) h16_A1354 conserved hypothetical protein
?AM260479 1464478 = 0 (0.000)coding (162/552 nt) h16_A1354 conserved hypothetical protein

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGAC  >  AM260479/1464304‑1464567
                                                                                                                                         |                                                                                                                              
gagatgtgtataagagacaGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTG                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:2101:7469:63797/131‑1 (MQ=60)
             ATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATG                                                                                                      >  GWNJ‑0478:712:GW2002102894th:2:1106:1634:8122/1‑150 (MQ=60)
                    CCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACC                                                                                                  >  GWNJ‑0478:712:GW2002102894th:2:2205:18402:48831/1‑147 (MQ=60)
                       acggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGC                                                                                             <  GWNJ‑0478:712:GW2002102894th:2:2113:18604:62230/94‑1 (MQ=60)
                         GACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACG                                                                                          >  GWNJ‑0478:712:GW2002102894th:2:1108:7005:61705/1‑150 (MQ=60)
                             ttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagTGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgc                                                                                        <  GWNJ‑0478:712:GW2002102894th:2:1210:6210:86554/73‑3 (MQ=38)
                                GTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGTCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTctgtctcttatacacatc                                                                                   >  GWNJ‑0478:712:GW2002102894th:2:2214:3563:38645/1‑132 (MQ=60)
                                  CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt                                                                                 <  GWNJ‑0478:712:GW2002102894th:2:2208:11971:45971/150‑10 (MQ=60)
                                  CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt                                                                                 <  GWNJ‑0478:712:GW2002102894th:2:2212:11302:74673/150‑10 (MQ=60)
                                           GTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTctgtctcttatacacatctccgagcccacgagacggagctacat                                                                        >  GWNJ‑0478:712:GW2002102894th:2:1109:14344:50570/1‑106 (MQ=60)
                                                                                                                   GTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaaaaagaaaa  >  GWNJ‑0478:712:GW2002102894th:2:1207:18615:34373/1‑58 (MQ=16)
                                                                                                                                         |                                                                                                                              
GACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGAC  >  AM260479/1464304‑1464567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑