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 F5 I179 R1
|
182 |
40.3 |
1547118 |
96.8% |
1497610 |
120.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
771,407 |
A→G |
T35A (ACA→GCA) |
tolR → |
colicin uptake protein TolR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 771,407 | 0 | A | G | 94.4%
| 54.5
/ ‑3.0
| 18 | T35A (ACA→GCA) | tolR | colicin uptake protein TolR |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (8/9); total (9/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTTTACCGTTAGCGAGAGCAACAAGGGGTAAGCCATGGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTA > NZ_CP009273/771271‑771515
|
gTTTACCGTTAGCGAGAGCAACAAGGGGTAAGCCATGGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCa < 2:100217/139‑1 (MQ=255)
ccGTTAGCGAGAGCAACAAGGGGTAAGCCATGGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGcc < 2:451481/139‑1 (MQ=255)
aaGCCATGGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGt > 2:401819/1‑139 (MQ=255)
ggCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTg > 2:317932/1‑139 (MQ=255)
gTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTAc > 1:339200/1‑139 (MQ=255)
cGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCAcc > 1:291130/1‑102 (MQ=255)
cGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCAcc < 2:291130/102‑1 (MQ=255)
ttGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGt < 1:46554/139‑1 (MQ=255)
ttGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCCGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGGGGAGGAACGAACATACGCCCGTGAttgttt > 2:238037/1‑138 (MQ=255)
ttGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGcc < 2:502769/50‑1 (MQ=255)
ttGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGcc > 1:502769/1‑50 (MQ=255)
ttGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAAAGATAATCCGCCAGTGAttgtt > 1:187272/1‑138 (MQ=255)
cTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGaa < 1:317932/138‑1 (MQ=255)
cTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGaa < 1:191884/138‑1 (MQ=255)
tACTGCTGGTGCTGTTGCTGATCTTTATGGCGACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTgg > 1:318175/1‑139 (MQ=255)
aCTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGGGAGGAGGAACGATAATCCGCCAGTGATTGTTGGAGTGTCTgg > 2:191884/1‑138 (MQ=255)
ctgctgGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTa < 2:187272/139‑1 (MQ=255)
ctgctgGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTa < 1:401819/139‑1 (MQ=255)
|
GTTTACCGTTAGCGAGAGCAACAAGGGGTAAGCCATGGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTA > NZ_CP009273/771271‑771515
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTAC > NZ_CP009273/771307‑771526
|
GGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCCGAGCGTGGAGGTCGATCTGCCAGACGCTACT > SRR3722133.343968/1‑151 (MQ=60)
GAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGActgtctcttatacacatctccgagccc > SRR3722133.295085/1‑124 (MQ=60)
agtacggtctcgtgggctcggagatgtgtataagagacagTTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAG < SRR3722133.211224/110‑1 (MQ=60)
ACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaaa > SRR3722133.509543/1‑72 (MQ=60)
ACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGGGAGCAGTAAAGATAATCCGCCAGTGATTGTTG > SRR3722133.189726/1‑150 (MQ=60)
ATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAG < SRR3722133.47138/151‑1 (MQ=60)
GTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGT > SRR3722133.322566/1‑151 (MQ=60)
GCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTAT < SRR3722133.194431/150‑1 (MQ=60)
GCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTAT < SRR3722133.322320/150‑1 (MQ=60)
ACTGCTGGTGCTGTTGCTGATCTTTATGGCGGCAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTAC < SRR3722133.407390/151‑1 (MQ=60)
|
GGCCAGAGCGCGTGGACGAGGTCGTCGCGATCTCAAGTCCGAAATCAACATTGTACCGTTGCTGGACGTACTGCTGGTGCTGTTGCTGATCTTTATGGCGACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTAC > NZ_CP009273/771307‑771526
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
