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 |
|
A2 F13 I0 R1
|
203 |
85.6 |
3649704 |
98.8% |
3605907 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
3,951,159 |
T→C |
100% |
intergenic (‑123/+72) |
PP_3486 ← / ← PP_3487 |
cytochrome c/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 3,951,159 | 0 | T | C | 100.0%
| 70.7
/ NA
| 21 | intergenic (‑123/+72) | PP_3486/PP_3487 | cytochrome c/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/3); total (18/3) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCG > NC_002947_CJ‑RC/3951030‑3951302
|
ttGCCATGCCAAGCACGCAGTTAAGCCAAATCGCAAGCCCTGGGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGc < 6:344058/149‑1 (MQ=38)
gCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGCTGCCACAGAGGCCAATTCCCCAGGCGGCCCATGa > 7:85974/1‑148 (MQ=255)
tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCacc > 8:48785/1‑148 (MQ=255)
cgAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCCCAGAGGCCAATTCCCCAGGCGGCCCATGATACTCaccgacc > 3:132984/1‑149 (MQ=255)
gCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGc > 5:313141/1‑149 (MQ=255)
tGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTACCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGACCATGATACACACCGACCCGCCAGCgg > 8:136935/1‑149 (MQ=255)
cGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCGCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGc > 1:131790/1‑149 (MQ=255)
ggCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCt > 8:338143/1‑149 (MQ=255)
aGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCa > 4:230003/1‑149 (MQ=255)
tGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATg > 6:118574/1‑149 (MQ=255)
gCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATgcg > 7:379741/1‑149 (MQ=255)
gCAGCTCAAGCGCAGAAAGAGGAGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATgcg > 5:196653/1‑149 (MQ=255)
cTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTGCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTgg < 7:136935/149‑1 (MQ=255)
gcgcAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCaa > 8:405511/1‑148 (MQ=255)
gcAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATcg > 1:130401/1‑149 (MQ=255)
agagGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTg > 6:239968/1‑149 (MQ=255)
cgcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGc > 5:250067/1‑148 (MQ=255)
gcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGt > 7:38563/1‑137 (MQ=255)
gcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGt < 8:38563/137‑1 (MQ=255)
gcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCg > 4:5491/1‑148 (MQ=255)
gcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCg > 1:14442/1‑148 (MQ=255)
|
TTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCG > NC_002947_CJ‑RC/3951030‑3951302
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGA > NC_002947_CJ‑RC/3951009‑3951303
|
gggcgggggtgtcggtcgatttgcccttgccaagcccgccgtaatccataatccgacgcctggtggttgcggccttggggcgctaacGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCC < NB501016:282:H2V7GAFX2:3:21509:1433:12043/64‑1 (MQ=60)
gtgttctcccccgggcccgcggggctttggggccggggggcccgccggttgggggggcggggcgtggcgcccccacggggcgcccccccccCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACG < NB501016:282:H2V7GAFX2:2:11311:15836:13577/60‑1 (MQ=60)
gacgtccccatcccacccacgctgtaacgccataccccaccccgtggggccgcggcctggcgtcgctaacgggcggcccacccGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCC < NB501016:282:H2V7GAFX2:4:21505:11941:15592/68‑1 (MQ=60)
agttgccctcccacacccggctgcaacccaaatccgcacgccgggggggcgcggcgtggcgccgctatcggggggcccacccGCCCCGGCAGTGGCAGCTCAAGCGCAGAACGAGGGCAGCGCTGCGC‑GCTCCTTCCGCGACGCAAGGCC < NB501016:282:H2V7GAFX2:2:11302:18520:8876/68‑1 (MQ=54)
GGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGCTGCCACAGAGGCCAATTCCCCAGGCGGCCCATGAT > NB501016:282:H2V7GAFX2:4:11501:12826:12230/1‑150 (MQ=60)
GTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAgggcttgcgatatggcttacctgcgtgcttggcatggcaacttcgacctc > NB501016:282:H2V7GAFX2:1:21203:10616:5241/1‑99 (MQ=60)
GCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCCCAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCC > NB501016:282:H2V7GAFX2:2:11210:22290:5383/1‑151 (MQ=60)
CGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCAGCCCTT‑TCGCGACGCAAGGCCGCTCCCACA > NB501016:282:H2V7GAFX2:2:11109:17565:7125/1‑95 (MQ=60)
GGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCG > NB501016:282:H2V7GAFX2:3:21501:23971:20343/1‑151 (MQ=60)
CCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCGCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCCATTCCCCAGGCGGCCCATGAGACTCACCGACCGGCCAGCGGCTGGGTCAACAGCT > NB501016:282:H2V7GAFX2:1:11208:8857:10433/1‑151 (MQ=60)
GGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGC > NB501016:282:H2V7GAFX2:4:21510:14523:12123/1‑151 (MQ=60)
GGCAGCTCAAGCGCAGAAAGAGGAGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGC > NB501016:282:H2V7GAFX2:3:11607:15276:5973/1‑151 (MQ=60)
GCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTGCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGG < NB501016:282:H2V7GAFX2:4:11509:5372:8445/151‑1 (MQ=60)
CGCAGAAAGAGGGGAGCGCTGCGC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGC > NB501016:282:H2V7GAFX2:1:11208:9546:6278/1‑151 (MQ=60)
GC‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCG > NB501016:282:H2V7GAFX2:3:21403:2640:12682/1‑150 (MQ=60)
C‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGA > NB501016:282:H2V7GAFX2:1:11103:15812:2307/1‑150 (MQ=60)
C‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTG > NB501016:282:H2V7GAFX2:4:11406:7018:15030/1‑139 (MQ=60)
|
GGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑GCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGA > NC_002947_CJ‑RC/3951009‑3951303
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
