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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
611,351 |
Δ1 bp |
coding (1739/3882 nt) |
entF → |
enterobactin non‑ribosomal peptide synthetase EntF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 611,348 | 0 | C | . | 100.0%
| 101.2
/ NA
| 23 | coding (1736/3882 nt) | entF | enterobactin non‑ribosomal peptide synthetase EntF |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (11/12); total (11/12) |
AAGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACGCCCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCT > NZ_CP009273/611258‑611428
|
aaGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACGc < 2:560019/91‑1 (MQ=255)
aGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACGcc < 2:786426/91‑1 (MQ=255)
cgtccgtcGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTac > 1:13052/1‑91 (MQ=255)
cgtccgtcGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTac < 2:389684/91‑1 (MQ=255)
acagcgacgaTTAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGcgccg > 1:37151/5‑91 (MQ=255)
accGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCt > 2:50703/1‑91 (MQ=255)
accGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCt > 1:247266/1‑91 (MQ=255)
acgaTCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCaa < 1:38211/91‑1 (MQ=255)
gCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAAc < 2:22721/91‑1 (MQ=255)
gcgcTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGc > 1:634907/1‑91 (MQ=255)
gcgcTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGc > 2:478779/1‑91 (MQ=255)
aGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCacac < 1:419704/91‑1 (MQ=255)
gATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGc < 1:834051/91‑1 (MQ=255)
aTGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCt < 1:804133/91‑1 (MQ=255)
aTGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCt < 1:193200/91‑1 (MQ=255)
gTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTta > 1:101445/1‑91 (MQ=255)
cccAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTatat < 2:368041/91‑1 (MQ=255)
cccAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTatat < 1:20731/91‑1 (MQ=255)
tAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCttt < 1:289818/91‑1 (MQ=255)
tAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCttt > 2:685997/1‑91 (MQ=255)
aGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGc < 2:250654/63‑1 (MQ=255)
aGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGc > 1:250654/1‑63 (MQ=255)
aGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCacac > 2:138581/1‑70 (MQ=255)
aGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCacac < 1:138581/70‑1 (MQ=255)
ttGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCt > 1:118840/1‑91 (MQ=255)
|
AAGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACGCCCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCT > NZ_CP009273/611258‑611428
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGAAGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACGCCCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCTCCACCGGCAGGCCGAAAGGGG > NZ_CP009273/611256‑611449
|
GGAAGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTAC > SRR3722118.13303/1‑101 (MQ=60)
gtggtaattaacagCGACGATTAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCG > SRR3722118.37828/15‑101 (MQ=60)
GTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCT > SRR3722118.252276/1‑101 (MQ=60)
ACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAAC < SRR3722118.38911/101‑1 (MQ=60)
ATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGC > SRR3722118.648597/1‑101 (MQ=60)
CTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTA > SRR3722118.103308/1‑101 (MQ=60)
ataagagacagCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATC < SRR3722118.141217/90‑1 (MQ=60)
AGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATC < SRR3722118.428564/101‑1 (MQ=60)
GATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCCTATATCATC < SRR3722118.852434/101‑1 (MQ=60)
ATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCT < SRR3722118.197028/101‑1 (MQ=60)
ATGTTCCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCT < SRR3722118.821790/101‑1 (MQ=60)
CCCAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACC < SRR3722118.21117/101‑1 (MQ=60)
CAATTTAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCctgtctcttatacacatc > SRR3722118.255754/1‑83 (MQ=60)
TAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCT < SRR3722118.295763/101‑1 (MQ=60)
TAACAAGCCTTTGCTATAACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCT > SRR3722118.121068/1‑101 (MQ=60)
ACG‑CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCTCCACCGGCAGGCCGAAAG < SRR3722118.700922/101‑1 (MQ=60)
cgCCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCTCCACCGGCAGGCCGAAAGG < SRR3722118.421933/99‑1 (MQ=60)
CCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCTCCACCGGCAGGCCGAAAGGGG > SRR3722118.568899/1‑101 (MQ=60)
|
GGAAGATGCGCGTCCGTCGCTGTTAATTACCACCGACGATCAACTGCCGCGCTTTAGCGATGTTCCCAATTTAACAAGCCTTTGCTATAACGCCCCGCTTACACCGCAGGGCAGTGCGCCGCTGCAACTTTCACAACCGCATCACACGGCTTATATCATCTTTACCTCTGGCTCCACCGGCAGGCCGAAAGGGG > NZ_CP009273/611256‑611449
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
