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
A0 F0 I1 R1 146 27.9 2327082 89.7% 2087392 107.8

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 30 [0] [0] 30 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)30 (1.090) 21/214 0.3 100% 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
CGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGACTGGCCTGATAA  >  AM260479/1464298‑1464578
                                                                                                                                               |                                                                                                                                         
CGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCAC                                                                                                                                    <  GWNJ‑0478:712:GW2002102894th:2:2215:6822:72158/150‑1 (MQ=60)
                GCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGG                                                                                                                    <  GWNJ‑0478:712:GW2002102894th:2:1204:19914:53368/150‑1 (MQ=60)
                 CCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGA                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:1111:7635:76758/150‑1 (MQ=60)
                   ATGCCCGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATG                                                                                                                 <  GWNJ‑0478:712:GW2002102894th:2:2205:1767:32687/150‑1 (MQ=60)
                       ACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACC                                                                                                             <  GWNJ‑0478:712:GW2002102894th:2:1103:18779:25999/150‑1 (MQ=60)
                       ACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACC                                                                                                             <  GWNJ‑0478:712:GW2002102894th:2:2205:17794:51487/150‑1 (MQ=60)
                             GTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGC                                                                                                        <  GWNJ‑0478:712:GW2002102894th:2:2201:18951:8958/149‑1 (MQ=60)
                                        CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt                                                                                            >  GWNJ‑0478:712:GW2002102894th:2:2201:15324:19331/1‑141 (MQ=60)
                                         gagatgtgtataagagacaggtccagcGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt                                                                                            <  GWNJ‑0478:712:GW2002102894th:2:2209:1567:15644/123‑10 (MQ=60)
                                                GGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggtctgtctct                                                                                    >  GWNJ‑0478:712:GW2002102894th:2:1210:5378:93042/1‑133 (MQ=60)
                                                                                              CTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATctgtctcttatacacatctccgagcccacgagacactcg  >  GWNJ‑0478:712:GW2002102894th:2:2111:19726:94460/1‑111 (MQ=57)
                                                                                                                                               |                                                                                                                                         
CGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGACTGGCCTGATAA  >  AM260479/1464298‑1464578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑