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 |
3,020,329 |
G→T |
intergenic (‑57/+6) |
rpoS ← / ← nlpD |
RNA polymerase sigma factor RpoS/murein hydrolase activator NlpD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,020,329 | 0 | G | T | 100.0%
| 88.7
/ NA
| 25 | intergenic (‑57/+6) | rpoS/nlpD | RNA polymerase sigma factor RpoS/murein hydrolase activator NlpD |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (22/3); total (22/3) |
ACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATT > NC_017635/3020285‑3020372
|
aCCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTcctccg > 1:2350416/1‑48 (MQ=255)
gTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGAttt < 1:443684/48‑1 (MQ=255)
tGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTa < 2:2038974/48‑1 (MQ=255)
gATCCCTTGCCGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTAt > 1:909514/1‑48 (MQ=255)
gATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTAt > 1:1051686/1‑48 (MQ=255)
gATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTAt > 2:292368/1‑48 (MQ=255)
tCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCg > 2:304411/1‑48 (MQ=255)
tCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCg > 2:2253/1‑48 (MQ=255)
ggAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCa > 2:621784/1‑47 (MQ=255)
aaCATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCaaa > 1:19122/1‑47 (MQ=255)
aaCATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCaaa > 2:1980445/1‑47 (MQ=255)
aCATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAAt > 1:1221988/1‑47 (MQ=255)
aCATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAAt > 1:1233153/1‑47 (MQ=255)
aTTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAAc > 1:530037/1‑48 (MQ=255)
aTTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAAc > 2:1900105/1‑48 (MQ=255)
tCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACg > 2:1907111/1‑47 (MQ=255)
tCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACg > 1:2504951/1‑47 (MQ=255)
cAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCgg > 2:240572/1‑48 (MQ=255)
aaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGtt > 2:125924/1‑48 (MQ=255)
aaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGtt > 1:2563313/1‑48 (MQ=255)
aaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGtt > 1:2581241/1‑48 (MQ=255)
aGCCTGGTTCCTCCGATTTAGCGCTGCGGCAAATAACGCAGCGGGttt < 1:1802253/48‑1 (MQ=39)
gCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTa > 1:1741728/1‑48 (MQ=255)
cTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACg > 2:242695/1‑48 (MQ=255)
cTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACg > 1:1497325/1‑48 (MQ=255)
ttCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAtt > 1:987265/1‑48 (MQ=255)
|
ACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATT > NC_017635/3020285‑3020372
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ 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
CCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTT > NC_017635/3020286‑3020379
|
CCCGTGATACCGTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTT < M01420:84:000000000‑ABVEH:1:2114:22038:22395/51‑1 (MQ=47)
CGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTAT < M01420:84:000000000‑ABVEH:1:1104:23850:22709/51‑1 (MQ=60)
GTGATCCCTTGCCGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATC > M01420:84:000000000‑ABVEH:1:1108:7013:22183/1‑51 (MQ=60)
GTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATC > M01420:84:000000000‑ABVEH:1:1110:15630:1598/1‑51 (MQ=60)
GGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAAT > M01420:84:000000000‑ABVEH:1:1101:15468:7523/1‑50 (MQ=60)
GAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATA > M01420:84:000000000‑ABVEH:1:1111:14023:13950/1‑50 (MQ=60)
GAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATA > M01420:84:000000000‑ABVEH:1:1111:5944:16042/1‑50 (MQ=60)
ACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACG > M01420:84:000000000‑ABVEH:1:1105:16990:16674/1‑51 (MQ=60)
ATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGC > M01420:84:000000000‑ABVEH:1:2108:14191:12918/1‑50 (MQ=60)
AAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTT > M01420:84:000000000‑ABVEH:1:2108:22357:24359/1‑51 (MQ=60)
AAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTT > M01420:84:000000000‑ABVEH:1:2109:12419:3435/1‑51 (MQ=60)
AAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTAC > M01420:84:000000000‑ABVEH:1:2101:7895:22278/1‑51 (MQ=60)
AAGCCTGGTTCCTCCGATTTAGCGCTGCGGCAAATAACGCAGCGGGTTTAC < M01420:84:000000000‑ABVEH:1:2102:2882:11626/51‑1 (MQ=60)
GCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGG > M01420:84:000000000‑ABVEH:1:1113:9390:20828/1‑51 (MQ=60)
GGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTT > M01420:84:000000000‑ABVEH:1:1109:3447:14380/1‑51 (MQ=60)
CCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCC > M01420:84:000000000‑ABVEH:1:2103:6389:23652/1‑51 (MQ=60)
CCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCC < M01420:84:000000000‑ABVEH:1:2109:12663:21443/50‑1 (MQ=60)
CCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTT < M01420:84:000000000‑ABVEH:1:2101:16507:2322/51‑1 (MQ=60)
|
CCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTT > NC_017635/3020286‑3020379
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
