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 F1 I1 R1
|
66 |
46.7 |
5280542 |
98.1% |
5180211 |
47.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
2,312,962 |
T→C |
G139G (GGA→GGG) |
ECW_RS11560 ← |
phage tail sheath protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 2,312,962 | 0 | T | C | 100.0%
| 48.4
/ NA
| 30 | G139G (GGA→GGG) | ECW_RS11560 | phage tail sheath protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/22); total (8/22) |
ACAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACC > NC_017635/2312920‑2313001
|
aCAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCg < 1:1155260/47‑1 (MQ=255)
aTGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACAcc > 2:675829/1‑46 (MQ=11)
ccAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCaaga < 1:1754046/47‑1 (MQ=11)
ccAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCaaga < 2:334973/47‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:1203715/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 2:885426/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 2:611327/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 2:590040/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 2:320801/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 2:2361106/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:620825/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:1356751/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:2185859/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:2258624/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:237836/48‑1 (MQ=11)
cAGTGCAACAGCCACCTCCTTGGTATCCAGCCCCGGCACACCAAGAAt < 1:1739519/48‑1 (MQ=11)
tGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAcg > 2:2389897/1‑48 (MQ=11)
gCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAcgc > 1:1311448/1‑48 (MQ=11)
gCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAcgc > 2:45403/1‑48 (MQ=11)
gCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAcgc > 2:259884/1‑48 (MQ=11)
gCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAcgc > 2:2312469/1‑48 (MQ=11)
gCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAcgc > 2:1668007/1‑48 (MQ=11)
aaCAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCgg < 2:191075/48‑1 (MQ=11)
aCAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGt < 1:2453886/48‑1 (MQ=11)
gCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTa < 2:1863582/48‑1 (MQ=11)
gCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTa < 2:843252/48‑1 (MQ=11)
gCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTa < 1:605305/48‑1 (MQ=11)
cACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAac < 2:2038753/48‑1 (MQ=11)
cACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAac < 2:1516810/48‑1 (MQ=11)
tATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTAcc > 1:446102/1‑47 (MQ=11)
|
ACAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACC > NC_017635/2312920‑2313001
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ 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
AGCTTCTGACAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACTCTGCCG > NC_017635/2312912‑2313011
|
AGCTTCTGACAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGC > M01420:84:000000000‑ABVEH:1:2109:23251:18128/1‑51 (MQ=14)
GACAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGC < M01420:84:000000000‑ABVEH:1:1110:16877:24283/50‑1 (MQ=13)
GCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAT < M01420:84:000000000‑ABVEH:1:2101:18717:25265/50‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:1103:10288:4158/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:2111:10636:14828/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:1106:20176:11674/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:1111:20079:10441/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:1112:6955:16798/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:2105:9952:19075/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:2106:12096:10888/51‑1 (MQ=11)
CCAGTGCAACAGCCACCTCCTTGGTATCCAGCCCCGGCACACCAAGAATAC < M01420:84:000000000‑ABVEH:1:2101:22232:21811/51‑1 (MQ=10)
GTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCG > M01420:84:000000000‑ABVEH:1:1112:11659:8125/1‑51 (MQ=11)
AACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTT < M01420:84:000000000‑ABVEH:1:2107:18773:26940/51‑1 (MQ=47)
AGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAAC > M01420:84:000000000‑ABVEH:1:2111:12648:9065/1‑51 (MQ=47)
AGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAAC < M01420:84:000000000‑ABVEH:1:1106:10475:8535/51‑1 (MQ=47)
GGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCG > M01420:84:000000000‑ABVEH:1:1104:15257:23241/1‑50 (MQ=8)
GTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACTCTGCCG > M01420:84:000000000‑ABVEH:1:2109:15841:7890/1‑51 (MQ=0)
|
AGCTTCTGACAGACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACTCTGCCG > NC_017635/2312912‑2313011
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
