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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
668,149 |
A→G |
N697N (AAT→AAC) |
leuS ← |
leucine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 668,149 | 0 | A | G | 100.0%
| 120.5
/ NA
| 33 | N697N (AAT→AAC) | leuS | leucine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/19); total (14/19) |
GGTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGATTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAG > NZ_CP009273/668068‑668236
|
ggTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTtcagtc < 2:317572/91‑1 (MQ=255)
ggTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTtcagtc < 2:339528/91‑1 (MQ=255)
tGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAgcgc < 2:1014490/91‑1 (MQ=255)
aGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAgcgcgcg < 1:172379/91‑4 (MQ=255)
gTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCaa < 2:333281/91‑1 (MQ=255)
gTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCaa < 1:618697/91‑1 (MQ=255)
tCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAAc > 2:25596/1‑91 (MQ=255)
tGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGt > 1:841621/1‑91 (MQ=255)
tGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGt > 1:768660/1‑91 (MQ=255)
acgacgGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTc < 1:513783/91‑1 (MQ=255)
acgacgGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTc < 2:360228/91‑1 (MQ=255)
acgacgGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTc < 1:166660/91‑1 (MQ=255)
atatCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCaa < 1:1039058/91‑1 (MQ=255)
tcatcGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACAt < 1:12857/91‑1 (MQ=255)
tCACTTTAGCGATCGTTTTATGCACATCGCGACGCCGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCttt > 2:492679/1‑91 (MQ=255)
ttAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCtg < 1:562961/91‑1 (MQ=255)
aTCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCt > 2:347377/1‑91 (MQ=255)
cGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCg > 1:803897/1‑91 (MQ=255)
cGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCg > 1:1006893/1‑91 (MQ=255)
cGTTTTAAGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCg > 1:1046161/1‑91 (MQ=255)
tGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCa < 1:884233/91‑1 (MQ=255)
cacaTCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGt < 1:342815/91‑1 (MQ=255)
caTCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGttt > 2:209202/1‑91 (MQ=255)
caTCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGttt > 2:113376/1‑91 (MQ=255)
aTCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTc > 2:107560/1‑91 (MQ=255)
tCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTcc > 2:544818/1‑91 (MQ=255)
gACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGac < 1:107560/91‑1 (MQ=255)
aCGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGaca > 2:255994/1‑91 (MQ=255)
aCGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGaca < 1:351766/91‑1 (MQ=255)
cAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGt > 1:293144/1‑91 (MQ=255)
tCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGaa < 2:768660/91‑1 (MQ=255)
cTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAg < 2:725048/91‑1 (MQ=255)
cTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAg < 2:947739/91‑1 (MQ=255)
|
GGTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGATTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAG > NZ_CP009273/668068‑668236
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
CCATAATCGCCGCAATTGCGGTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGATTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAGCGGTTAGCCCCT > NZ_CP009273/668049‑668248
|
CCATAATCGCCGCAATTGCGGTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGG > SRR3722125.289212/1‑101 (MQ=60)
CCATAATCGCCGCAATTGCGGTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGG > SRR3722125.206693/1‑101 (MQ=60)
GTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGT > SRR3722125.785344/1‑101 (MQ=60)
GTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGT > SRR3722125.860148/1‑101 (MQ=60)
TGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTN < SRR3722125.584425/101‑1 (MQ=60)
AGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCgcggtgtttgaag < SRR3722125.175722/101‑14 (MQ=60)
GTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGC < SRR3722125.632039/101‑1 (MQ=60)
ACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAA < SRR3722125.169847/101‑1 (MQ=60)
ACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAA < SRR3722125.524693/101‑1 (MQ=60)
ATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTT < SRR3722125.1062367/101‑1 (MQ=60)
TCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGC < SRR3722125.13103/101‑1 (MQ=60)
CTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCG > SRR3722125.1029409/1‑101 (MQ=60)
CTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCG > SRR3722125.821495/1‑101 (MQ=60)
CTTTAGCGATCGTTTTAAGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCG > SRR3722125.1069646/1‑101 (MQ=60)
TTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTA < SRR3722125.575009/101‑1 (MQ=60)
ATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTctgtctcttatacacatctccga > SRR3722125.774433/1‑78 (MQ=60)
ATGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGctgtctcttatacacatctccgagcccacgagactaggcatgatctc > SRR3722125.458658/1‑54 (MQ=60)
TGCACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGAC < SRR3722125.903787/101‑1 (MQ=60)
CACATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACAC < SRR3722125.349940/101‑1 (MQ=60)
CATCGCGACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGT > SRR3722125.299118/1‑101 (MQ=60)
GACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGG < SRR3722125.109595/101‑1 (MQ=60)
ACGCAGCGCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGA < SRR3722125.359118/101‑1 (MQ=60)
GCTTTCTGGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAGCGGTT > SRR3722125.520144/1‑101 (MQ=60)
GGTTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAGCGGTTAGCCCCT > SRR3722125.310012/1‑101 (MQ=60)
|
CCATAATCGCCGCAATTGCGGTGTTGAAGGTCTGACGACGGCCGATATCATCGGTCACTTTAGCGATCGTTTTATGCACATCGCGACGCAGCGCTTTCTGATTTTCAGTCAGCGCATCAACGTTCAGTGCCGCAACATCACCTTTTGCTGTGTGCTCGTAAACCAGTTTCCAGACACGTTTCAGGAAGCGGTTAGCCCCT > NZ_CP009273/668049‑668248
|
| 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: ‑ |
