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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,888,711 |
A→G |
V143A (GTC→GCC) |
ygcQ ← |
electron transfer flavoprotein subunit alpha/FixB family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,888,711 | 0 | A | G | 100.0%
| 81.5
/ NA
| 25 | V143A (GTC→GCC) | ygcQ | electron transfer flavoprotein subunit alpha/FixB family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/9); total (16/9) |
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAA > NZ_CP009273/2888625‑2888782
|
gCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCaa < 2:603465/90‑1 (MQ=255)
ccGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGtt > 1:47227/1‑90 (MQ=255)
cTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAgt < 2:207358/90‑1 (MQ=255)
ggCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAgttg > 1:105386/1‑90 (MQ=255)
ggCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAgttg > 2:100941/1‑90 (MQ=255)
cAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCa > 1:607260/1‑90 (MQ=255)
cAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCa > 1:329319/1‑90 (MQ=255)
aGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCAt < 2:583616/90‑1 (MQ=255)
aaTGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCa > 1:24787/1‑90 (MQ=255)
aaTGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCa > 2:262456/1‑90 (MQ=255)
gTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAggg > 1:478150/1‑90 (MQ=255)
gTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAggg > 1:527274/1‑90 (MQ=255)
tCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGc > 2:530822/1‑90 (MQ=255)
aCATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCg > 2:521032/1‑90 (MQ=255)
ttCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTc > 1:198368/1‑90 (MQ=255)
cAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCgc < 1:100941/90‑1 (MQ=255)
ccTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTc < 2:281246/90‑1 (MQ=255)
tctGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTccc > 1:79942/1‑90 (MQ=255)
ctGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCg > 1:574555/1‑90 (MQ=255)
gtgCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGcc > 1:453402/1‑90 (MQ=255)
tAACCAGCCAGTCCGGAAGCGCCCCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGAc < 1:262456/90‑1 (MQ=255)
tAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGAc < 2:618537/90‑1 (MQ=255)
cagccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGc < 2:441565/43‑1 (MQ=255)
cagccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGc > 1:441565/1‑43 (MQ=255)
tCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGaa < 2:173271/90‑1 (MQ=255)
|
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAA > NZ_CP009273/2888625‑2888782
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGA > NZ_CP009273/2888619‑2888781
|
CCACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTT > SRR3722112.47806/1‑100 (MQ=60)
CACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTC < SRR3722112.379520/100‑1 (MQ=60)
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTG > SRR3722112.106698/1‑100 (MQ=60)
CGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCA > SRR3722112.333265/1‑100 (MQ=60)
CGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCA > SRR3722112.616571/1‑100 (MQ=60)
GGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCA > SRR3722112.25102/1‑100 (MQ=60)
CAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGG > SRR3722112.485003/1‑100 (MQ=60)
CAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGG > SRR3722112.535064/1‑100 (MQ=60)
GGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTC > SRR3722112.200780/1‑100 (MQ=60)
TTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCC > SRR3722112.80922/1‑100 (MQ=60)
TTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCG > SRR3722112.583315/1‑100 (MQ=60)
CAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCC < SRR3722112.102200/100‑1 (MQ=60)
CAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCC > SRR3722112.459771/1‑100 (MQ=60)
CTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGctgtctcttatacacatctgacgctgccgacgaatgt > SRR3722112.447678/1‑63 (MQ=60)
TACCCAGCCAGTCCGGAAGCGCCCCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGA < SRR3722112.265541/100‑1 (MQ=60)
|
CCACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGA > NZ_CP009273/2888619‑2888781
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
