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 |
|
A0 F0 I1 R1
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,841,812 |
G→A |
G12S (GGC→AGC) |
gorA → |
glutathione‑disulfide reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,841,812 | 0 | G | A | 100.0%
| 63.9
/ NA
| 18 | G12S (GGC→AGC) | gorA | glutathione‑disulfide reductase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (9/9); total (9/9) |
AAGGACACTTTGTCATGACTAAACACTATGATTACATCGCCATCGGCGGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACGG > NC_017635/3841765‑3841858
|
aaGGACACTTTGTCATGACTAAACACTATGATTACATCGCCATcggcagc > 1:1947969/1‑50 (MQ=255)
gACACTTTGTCATGACTAAACACTATGATTACATCGCCATCggcagcggc < 2:1307341/50‑1 (MQ=255)
acTTTGTCATGACTAAACACTATGATTACATCGCCATCggcagcggcagc > 1:961586/1‑50 (MQ=255)
tGTCATGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAgcggcg > 2:603477/1‑50 (MQ=255)
tGTCATGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAgcggcg > 1:1597136/1‑50 (MQ=255)
aTGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTa < 1:205725/49‑1 (MQ=255)
aTGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTAt > 1:2022702/1‑50 (MQ=255)
tAAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGGATCGccc > 2:1703881/1‑49 (MQ=38)
aaCACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTc < 1:178653/49‑1 (MQ=255)
aaCACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTc > 1:24543/1‑49 (MQ=255)
aaCACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTc < 1:468296/49‑1 (MQ=255)
aaCACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTc > 1:720665/1‑49 (MQ=255)
aaCACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGAATCGCcccc > 2:1028514/1‑50 (MQ=38)
acTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATc < 2:1912405/50‑1 (MQ=255)
acTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATc < 1:1463036/50‑1 (MQ=255)
cTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCa < 1:449483/50‑1 (MQ=255)
tATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCaa > 2:713784/1‑50 (MQ=255)
gATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCAACcg > 1:1702560/1‑50 (MQ=255)
aTCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGc < 1:41863/50‑1 (MQ=255)
gCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGCTa < 2:1298324/49‑1 (MQ=255)
cATCGGCAGCGGCAGCGGCAGTATCGCCTCCATCAACCGCGCGGCTATGt < 2:1716218/50‑1 (MQ=39)
ggcagcggcagcGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACgg > 1:89269/1‑50 (MQ=255)
ggcagcggcagcGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACg < 2:143449/49‑1 (MQ=255)
ggcagcggcagcGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACg < 2:1038809/49‑1 (MQ=255)
ggcagcggcagcGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACg < 2:298041/49‑1 (MQ=255)
|
AAGGACACTTTGTCATGACTAAACACTATGATTACATCGCCATCGGCGGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACGG > NC_017635/3841765‑3841858
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAGGACACTTTGTCATGACTAAACACTATGATTACATCGCCATCGGCGGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACGGC > NC_017635/3841765‑3841859
|
AAGGACACTTTGTCATGACTAAACACTATGATTACATCGCCATCGGCAGCG > M01420:85:000000000‑AC936:1:2113:14247:10079/1‑51 (MQ=60)
ACTTTGTCATGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAGCG > M01420:85:000000000‑AC936:1:1114:21324:3169/1‑51 (MQ=60)
TGTCATGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGG > M01420:85:000000000‑AC936:1:2108:23716:18126/1‑51 (MQ=60)
CATGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTA < M01420:85:000000000‑AC936:1:1103:5435:21359/50‑1 (MQ=60)
ATGACTAAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATC > M01420:85:000000000‑AC936:1:2114:9178:9264/1‑51 (MQ=60)
AAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTC < M01420:85:000000000‑AC936:1:1103:6483:13254/50‑1 (MQ=60)
AAACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTC < M01420:85:000000000‑AC936:1:1107:4239:11003/50‑1 (MQ=60)
AACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCC > M01420:85:000000000‑AC936:1:1101:22062:11584/1‑50 (MQ=60)
AACACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCC > M01420:85:000000000‑AC936:1:1110:14420:20811/1‑50 (MQ=60)
CACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATC < M01420:85:000000000‑AC936:1:2106:26874:22605/51‑1 (MQ=60)
ACTATGATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCA < M01420:85:000000000‑AC936:1:1107:14915:4162/51‑1 (MQ=60)
GATTACATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCAACCGC > M01420:85:000000000‑AC936:1:2110:12966:3749/1‑51 (MQ=60)
CATCGCCATCGGCAGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGC < M01420:85:000000000‑AC936:1:1101:26127:16737/51‑1 (MQ=60)
GGCAGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACGGC > M01420:85:000000000‑AC936:1:1102:13277:8513/1‑51 (MQ=60)
|
AAGGACACTTTGTCATGACTAAACACTATGATTACATCGCCATCGGCGGCGGCAGCGGCGGTATCGCCTCCATCAACCGCGCGGCTATGTACGGC > NC_017635/3841765‑3841859
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
