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 |
609,731 |
A→G |
D40G (GAT→GGT) |
entF → |
enterobactin non‑ribosomal peptide synthetase EntF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 609,731 | 0 | A | G | 89.7%
| 69.4
/ 2.9
| 29 | D40G (GAT→GGT) | entF | enterobactin non‑ribosomal peptide synthetase EntF |
| Reads supporting (aligned to +/- strand): ref base A (0/3); new base G (12/14); total (12/17) |
| Fisher's exact test for biased strand distribution p-value = 2.46e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.20e-01 |
GCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAA > NZ_CP009273/609645‑609816
|
gCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTc > 1:263018/1‑90 (MQ=255)
gCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTc < 1:459900/90‑1 (MQ=255)
cGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAAGCGGAGAGGTTGGTTCGcc > 1:748405/1‑90 (MQ=255)
cGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGcc < 1:251176/90‑1 (MQ=255)
cGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGcc < 2:138944/90‑1 (MQ=255)
tGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTg > 2:401319/1‑90 (MQ=255)
aTGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGcc < 2:560679/90‑1 (MQ=255)
aGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCcgcgc < 1:157679/90‑1 (MQ=255)
aGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCcgcgc < 1:146073/90‑1 (MQ=255)
tGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTg > 2:96381/1‑90 (MQ=255)
aaTTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGAc < 2:164159/90‑1 (MQ=255)
ccTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAgcgc < 1:265830/90‑1 (MQ=255)
ccTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAgcgc < 1:292092/90‑1 (MQ=255)
tCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCaa < 2:509075/90‑1 (MQ=255)
ccGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAg > 1:738747/1‑90 (MQ=255)
tGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGAt < 2:231995/90‑1 (MQ=255)
gAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATAc < 2:579346/90‑1 (MQ=255)
gCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGc < 2:263018/90‑1 (MQ=255)
gCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGc > 2:462084/1‑90 (MQ=255)
cGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCt > 2:481071/1‑90 (MQ=255)
gTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAgcgc > 1:440446/1‑76 (MQ=255)
gTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAgcgc < 2:440446/76‑1 (MQ=255)
aTTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGc < 1:460067/90‑1 (MQ=255)
ttACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCg > 2:819257/1‑90 (MQ=255)
tGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTAc < 1:252144/90‑1 (MQ=255)
aaCCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGa > 1:478606/1‑90 (MQ=255)
aCCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGAt < 1:433269/90‑1 (MQ=255)
aCCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGAt > 1:151929/1‑90 (MQ=255)
ggttggttCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGa < 1:341341/90‑1 (MQ=255)
gTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGaa > 1:730852/1‑90 (MQ=255)
|
GCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAA > NZ_CP009273/609645‑609816
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
TCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAAGTCTGGCAG > NZ_CP009273/609635‑609825
|
TCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTC > SRR3722079.265220/1‑100 (MQ=60)
CCTCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAAGCGGAGAGGTTGGTTCGCC > SRR3722079.756401/1‑100 (MQ=60)
GCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTG < SRR3722079.463927/100‑1 (MQ=60)
CGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCC < SRR3722079.253280/100‑1 (MQ=60)
AGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCC < SRR3722079.147335/100‑1 (MQ=60)
AGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCC < SRR3722079.159048/100‑1 (MQ=60)
GAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAG > SRR3722079.746640/1‑100 (MQ=60)
CCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATAC < SRR3722079.268060/100‑1 (MQ=60)
CCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATAC < SRR3722079.294497/100‑1 (MQ=60)
CGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACctgt > SRR3722079.444276/1‑96 (MQ=60)
ATTACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGA < SRR3722079.464094/100‑1 (MQ=60)
ACGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGA > SRR3722079.482799/1‑100 (MQ=60)
CGTTGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGAT > SRR3722079.153243/1‑100 (MQ=60)
TGAGTTAACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAAC < SRR3722079.254256/100‑1 (MQ=60)
AACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAA > SRR3722079.738671/1‑100 (MQ=60)
ACCGGAGAGGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAAG < SRR3722079.437024/100‑1 (MQ=60)
GGTTGGTTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAAGTCTGGCAG < SRR3722079.344040/100‑1 (MQ=60)
|
TCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTGCGGATGCGTTTTACGGAAGATAACGGCGAAGTCTGGCAG > NZ_CP009273/609635‑609825
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
