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 F2 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,350,381 |
G→C |
G457G (GGC→GGG) |
cadC ← |
lysine decarboxylation/transport transcriptional activator CadC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,350,381 | 0 | G | C | 83.0%
| 127.8
/ 20.6
| 47 | G457G (GGC→GGG) | cadC | lysine decarboxylation/transport transcriptional activator CadC |
| Reads supporting (aligned to +/- strand): ref base G (4/4); new base C (17/22); total (21/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
GGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350296‑4350465
|
gggTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCaa > 1:785997/1‑90 (MQ=255)
gtgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGc < 2:785997/90‑1 (MQ=255)
tgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa > 2:184272/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 1:154015/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa < 1:740457/90‑1 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa < 2:21332/90‑1 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 1:257133/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 2:804486/1‑90 (MQ=255)
gCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAAcaca < 2:556601/90‑1 (MQ=255)
gCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAAcaca < 1:68646/90‑1 (MQ=255)
cccTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATa > 2:573599/1‑90 (MQ=255)
cccTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATa > 2:821339/1‑90 (MQ=255)
cTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAt > 1:82149/1‑90 (MQ=255)
tGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 2:340599/90‑1 (MQ=255)
gTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGcc > 1:829273/1‑90 (MQ=255)
gTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGcc > 1:209952/1‑90 (MQ=255)
tAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCa > 2:201602/1‑90 (MQ=255)
ttAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGAc < 1:195088/90‑1 (MQ=255)
ttAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGAc < 1:631597/90‑1 (MQ=255)
cGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCaa < 2:257133/90‑1 (MQ=255)
ggTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGc < 1:800930/61‑1 (MQ=255)
ggTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGc > 2:800930/1‑61 (MQ=255)
agaTATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCa < 2:353340/90‑1 (MQ=255)
cATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAg < 2:615021/90‑1 (MQ=255)
aTCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGt < 2:829273/90‑1 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTACAAGATCAATGCCAGTAtt > 1:466934/1‑90 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAtt > 2:707261/1‑90 (MQ=255)
gctgctTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAttt > 1:686423/1‑90 (MQ=255)
gctgctTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAAcaca < 1:593822/51‑1 (MQ=255)
gctgctTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAAcaca > 2:593822/1‑51 (MQ=255)
gctgctTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAttt > 2:488/1‑90 (MQ=255)
tgctTCCCGGTTCATCCCCTTCATTTTATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTAt < 1:660152/90‑1 (MQ=255)
tCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGcc < 1:676176/90‑1 (MQ=255)
cccGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCt < 2:82149/90‑1 (MQ=255)
cccGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCt < 1:363927/90‑1 (MQ=255)
tCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAg > 2:252944/1‑90 (MQ=255)
tCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAg < 1:707261/90‑1 (MQ=255)
tCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACt > 2:101745/1‑90 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 1:239372/90‑1 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 1:233689/90‑1 (MQ=255)
tttcatAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttt > 2:323225/1‑90 (MQ=255)
aaaCCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctt < 2:686423/90‑1 (MQ=255)
aCCTTGCCAAGCAACACATAATTTAGCCAGGACATTACAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 2:466934/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 1:377371/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 2:651431/90‑1 (MQ=255)
cTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCa < 2:483885/43‑1 (MQ=255)
cTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCa > 1:483885/1‑43 (MQ=255)
|
GGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350296‑4350465
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCACTGAC > NZ_CP009273/4350286‑4350479
|
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAA > SRR3722079.794423/1‑100 (MQ=60)
gagacagAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGC < SRR3722079.836057/93‑1 (MQ=60)
AGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAA > SRR3722079.155353/1‑100 (MQ=60)
AGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAA > SRR3722079.259294/1‑100 (MQ=60)
AAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACAC < SRR3722079.609042/100‑1 (MQ=60)
agatgtgtataagagacagAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAT < SRR3722079.809512/81‑1 (MQ=60)
GTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAT > SRR3722079.82812/1‑100 (MQ=60)
GTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTT < SRR3722079.748374/100‑1 (MQ=60)
gtgggctcggagatgtgtataagagacAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCC < SRR3722079.599767/73‑1 (MQ=60)
GCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCC > SRR3722079.838151/1‑100 (MQ=60)
GCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCC < SRR3722079.69210/100‑1 (MQ=60)
GCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCC > SRR3722079.211747/1‑100 (MQ=60)
TTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGAT < SRR3722079.638056/100‑1 (MQ=60)
TTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGAT < SRR3722079.196771/100‑1 (MQ=60)
GATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTACAAGATCAATGCCAGTATT > SRR3722079.471017/1‑100 (MQ=60)
ATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTT > SRR3722079.693636/1‑100 (MQ=60)
TGCTTCCCGGTTCATCCCCTTCATTTTATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAA < SRR3722079.667008/100‑1 (MQ=60)
TCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACT < SRR3722079.683271/100‑1 (MQ=60)
CCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTC < SRR3722079.366781/100‑1 (MQ=60)
TCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGT < SRR3722079.714769/100‑1 (MQ=60)
CTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCT < SRR3722079.241390/100‑1 (MQ=60)
CTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCT < SRR3722079.235667/100‑1 (MQ=60)
TTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATctgtctcttatacacatctccgagcccacgagaccag > SRR3722079.488108/1‑63 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722079.380432/100‑1 (MQ=60)
TCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCACTGAC < SRR3722079.494/100‑1 (MQ=60)
|
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCACTGAC > NZ_CP009273/4350286‑4350479
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
