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 152 24.9 2083062 91.6% 1908084 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
MC JC AM260479 3,376,159 (CGGTGGCGCTCG)2→1 coding (378‑389/1146 nt) phcR ← signal transduction histidine kinase containing a receiver domain (hybrid)

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ AM260479 3376140 3376151 12 21 [0] [0] 25 phcR signal transduction histidine kinase containing a receiver domain (hybrid)

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AM260479 3376152 =0 (0.000)19 (0.940) 15/178 0.3 100% coding (396/1146 nt) phcR signal transduction histidine kinase containing a receiver domain (hybrid)
?AM260479 = 3376139 0 (0.000)coding (409/1146 nt) phcR signal transduction histidine kinase containing a receiver domain (hybrid)

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATG  >  AM260479/3376072‑3376296
                                                                                       |                                                                                                                                         
GTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACtgtctcttatacacatctccgagcccac                                                                 >  GWNJ‑0478:712:GW2002102894th:2:2116:17579:7290/1‑122 (MQ=60)
  ATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGAC                                                               >  GWNJ‑0478:712:GW2002102894th:2:2209:16395:89031/1‑150 (MQ=60)
       gtgttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATG                                                                       <  GWNJ‑0478:712:GW2002102894th:2:2212:16964:44930/70‑1 (MQ=60)
                 CAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGAC                                                <  GWNJ‑0478:712:GW2002102894th:2:1112:2344:51517/150‑1 (MQ=60)
                    GAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGT                                             <  GWNJ‑0478:712:GW2002102894th:2:2104:8112:50004/150‑1 (MQ=60)
                              cgtctcgtgggctcggagatgtgtataagagacaggtgctggcgcagggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACC                                               <  GWNJ‑0478:712:GW2002102894th:2:1204:6667:59421/100‑1 (MQ=60)
                              GTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGctgtctcttatacacatctccgagcccacgagacggagct                                   >  GWNJ‑0478:712:GW2002102894th:2:2112:11459:97747/1‑110 (MQ=60)
                                           CCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACctgtctcttatacacatctccgagcccacgagacggagct                       >  GWNJ‑0478:712:GW2002102894th:2:2206:18340:99114/1‑109 (MQ=60)
                                           CCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGG                      >  GWNJ‑0478:712:GW2002102894th:2:2205:8440:78451/1‑150 (MQ=60)
                                               CAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCAT                   <  GWNJ‑0478:712:GW2002102894th:2:1210:19067:93074/149‑1 (MQ=60)
                                                                      ggcgcagggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGActgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttg       >  GWNJ‑0478:712:GW2002102894th:2:1111:20671:54572/11‑84 (MQ=60)
                                                                        cgcagggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGG     <  GWNJ‑0478:712:GW2002102894th:2:2207:17425:69710/142‑1 (MQ=60)
                                                                           agggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATG  <  GWNJ‑0478:712:GW2002102894th:2:2111:12165:65039/145‑1 (MQ=60)
                                                                                       |                                                                                                                                         
GTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATG  >  AM260479/3376072‑3376296

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑