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 F33 I1 R1 16 30.3 1339016 95.2% 1274743 112.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
MC JC NC_000913 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 4001645 4001649 5 35 [0] [0] 35 corA magnesium/nickel/cobalt transporter

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 40016440 (0.000)35 (1.160) 33/222 0.1 100% coding (219/951 nt) corA magnesium/nickel/cobalt transporter
?NC_000913 4001650 = 0 (0.000)coding (225/951 nt) corA magnesium/nickel/cobalt transporter

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ACGACGAGCGACTGCGCGTACAATCTGAACTTGGCCAGAGCCTGGCAACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCATATTCACTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGATGGTCGTCTGTTTACTCTGCGTGAGCGTGAACTGCCCGCTTTTCGTCTGTATCGTAT  >  NC_000913/4001532‑4001775
                                                                                                                 |                                                                                                                                  
ACGACGAGCGACTGCGCGTACAATCTGAACTTGGCCAGAGCCTGGCAACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCT                                                                                                                     >  NB501016:228:HFK2FAFXY:1:11208:7918:8281/1‑124 (MQ=60)
                      ATCTGAACTTGGCCAGAGCCTGGCAACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCT                                                                                                                        >  NB501016:228:HFK2FAFXY:1:21108:24439:11238/1‑99 (MQ=60)
                               TGGCCAGAGCCTGGCAACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTG                                                                              <  NB501016:228:HFK2FAFXY:4:11506:23084:4311/132‑1 (MQ=60)
                                atacgagatacgaattcgtgactggagttcagacgtgtgctcttccgaatctGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGAT                                                          <  NB501016:228:HFK2FAFXY:2:21211:17567:2928/99‑1 (MQ=60)
                                           GGCAACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGATGGTCGTCTG                                                 <  NB501016:228:HFK2FAFXY:1:11311:16312:2961/149‑1 (MQ=60)
                                               ACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCacggatggtaaat                                                   >  NB501016:228:HFK2FAFXY:2:21205:17442:19712/1‑130 (MQ=60)
                                                CCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCG                                                                                                       <  NB501016:228:HFK2FAFXY:1:11103:11287:6980/90‑1 (MQ=60)
                                                    CCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGAT                                                          >  NB501016:228:HFK2FAFXY:1:11205:15033:2759/1‑131 (MQ=60)
                                                         AACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGATGGTCGTCTGTTTACTCTGCG                                      <  NB501016:228:HFK2FAFXY:1:21311:24660:3508/146‑1 (MQ=60)
                                                             GGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCA                                                                         >  NB501016:228:HFK2FAFXY:3:11606:25156:14150/1‑107 (MQ=60)
                                                               AAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTG                                                                                                               >  NB501016:228:HFK2FAFXY:2:11202:17248:19042/1‑67 (MQ=60)
                                                                   CATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCAgatcggaagaagcacacgtctgaactccagtcacgaattcgtatctcgtatgccgtcttctgcttgaaaaa                        >  NB501016:228:HFK2FAFXY:4:11507:14101:15668/1‑79 (MQ=60)
                                                                   CATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGG                                                                           <  NB501016:228:HFK2FAFXY:4:11511:9628:9176/99‑1 (MQ=60)
                                                                    ATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCacggatggtaaatgccacagtgg                                         >  NB501016:228:HFK2FAFXY:2:11309:16196:19291/1‑109 (MQ=60)
                                                                                       TCTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAA                                                                                                             <  NB501016:228:HFK2FAFXY:4:21608:14353:13428/45‑1 (MQ=41)
                                                                                        CTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAGCTCCACTGTGGCATTTACCATCCGTGATGGTCGTCTGTTTACTCTGCGTGAGCGTGAACTGCCCGCTTTTCGTCTGTATCGTAT  >  NB501016:228:HFK2FAFXY:1:21207:16244:12368/1‑151 (MQ=60)
                                                                                        CTTTGAAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGT                                                                                        <  NB501016:228:HFK2FAFXY:1:21307:2775:9134/65‑1 (MQ=60)
                                                                                             AAGACGACGACGGCCTGCAT‑‑‑‑‑CTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGATGGTC                                                      <  NB501016:228:HFK2FAFXY:2:11107:2928:4553/94‑1 (MQ=60)
                                                                                                                 |                                                                                                                                  
ACGACGAGCGACTGCGCGTACAATCTGAACTTGGCCAGAGCCTGGCAACCCGCCCGGAACTGGAAGACATCGAAGCATCGGCACGTTTCTTTGAAGACGACGACGGCCTGCATATTCACTCCTTCTTCTTCTTTGAAGATGCGGAAGATCACGCCGGTAACTCCACTGTGGCATTTACCATCCGTGATGGTCGTCTGTTTACTCTGCGTGAGCGTGAACTGCCCGCTTTTCGTCTGTATCGTAT  >  NC_000913/4001532‑4001775

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑