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 |
3,020,329 |
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%
| 188.8
/ NA
| 51 | 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 (22/29); total (22/29) |
CTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTC > NC_017635/3020283‑3020374
|
cTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTtcctcc < 1:1543025/49‑1 (MQ=255)
tACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGa > 2:1425556/1‑50 (MQ=255)
tACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGa > 2:1646447/1‑50 (MQ=255)
cccGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGa < 2:473138/48‑1 (MQ=255)
cccGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGAt < 1:587977/49‑1 (MQ=255)
ccGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGAttt < 2:983608/50‑1 (MQ=255)
ccGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGAttt < 1:141218/50‑1 (MQ=255)
tGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATc < 1:756706/50‑1 (MQ=255)
tGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATc < 2:1072446/50‑1 (MQ=255)
tGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATc < 1:1515448/50‑1 (MQ=255)
aTCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCg < 2:998426/49‑1 (MQ=255)
aTCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGc > 1:1609643/1‑50 (MQ=255)
ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGc > 2:191429/1‑50 (MQ=255)
ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGc > 2:2041397/1‑50 (MQ=255)
ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGc > 2:414794/1‑50 (MQ=255)
ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGc > 2:121309/1‑50 (MQ=255)
ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGc > 2:1125783/1‑50 (MQ=255)
ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGc > 1:711841/1‑50 (MQ=255)
cTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCg > 2:1586878/1‑50 (MQ=255)
cTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCg < 2:466322/50‑1 (MQ=255)
cTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCg > 2:1171155/1‑50 (MQ=255)
tGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCgg > 2:1034258/1‑49 (MQ=255)
cGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCaaa < 1:1100805/50‑1 (MQ=255)
ggAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCaaa > 2:775229/1‑49 (MQ=255)
ggAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAAt < 2:992802/50‑1 (MQ=255)
gAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAAt > 1:1054260/1‑49 (MQ=255)
gAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATa < 1:1294373/50‑1 (MQ=255)
gAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATa < 2:501406/50‑1 (MQ=255)
aaCATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATaa < 1:842613/50‑1 (MQ=255)
cATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACg < 2:566318/50‑1 (MQ=255)
aTTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACg > 1:663310/1‑49 (MQ=255)
cAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAg < 1:162211/49‑1 (MQ=255)
cAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGc > 2:50217/1‑50 (MQ=255)
aaGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCg < 2:357771/50‑1 (MQ=255)
aaGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCg < 1:26836/50‑1 (MQ=255)
gCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCggg > 1:1421689/1‑50 (MQ=255)
aaaaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGtt > 2:2025860/1‑50 (MQ=255)
aaaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGttt < 1:1070030/50‑1 (MQ=255)
aaaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGtt > 1:438286/1‑49 (MQ=255)
aaGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTa < 1:1898565/50‑1 (MQ=255)
aGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTAc < 1:1208850/50‑1 (MQ=255)
aGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTAc < 2:745783/50‑1 (MQ=255)
gCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACg < 2:13017/50‑1 (MQ=255)
ccTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACgg < 1:1128069/50‑1 (MQ=255)
ccTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACgg < 2:1936463/50‑1 (MQ=255)
ccTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACgg < 1:1083420/50‑1 (MQ=255)
tGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAt > 2:2049914/1‑50 (MQ=255)
tGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAt > 1:940087/1‑50 (MQ=255)
ggTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAtt > 2:374963/1‑50 (MQ=255)
gTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAttt < 2:154926/50‑1 (MQ=255)
gTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAt < 1:321158/48‑1 (MQ=255)
ttCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTc < 2:2047401/50‑1 (MQ=255)
|
CTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTC > NC_017635/3020283‑3020374
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCT > NC_017635/3020279‑3020378
|
GCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCT < M01420:85:000000000‑AC936:1:1110:18374:21851/51‑1 (MQ=60)
CCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCC < M01420:85:000000000‑AC936:1:2107:18145:24844/50‑1 (MQ=60)
ACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGAT < M01420:85:000000000‑AC936:1:1108:19206:26044/50‑1 (MQ=60)
CCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTT < M01420:85:000000000‑AC936:1:1102:18936:24847/51‑1 (MQ=60)
GTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATC < M01420:85:000000000‑AC936:1:2107:8242:15854/51‑1 (MQ=60)
GTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATC < M01420:85:000000000‑AC936:1:1111:12716:9541/51‑1 (MQ=60)
ATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCT > M01420:85:000000000‑AC936:1:2108:4627:22046/1‑51 (MQ=60)
CCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCG > M01420:85:000000000‑AC936:1:1110:15886:18068/1‑51 (MQ=60)
ACGGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAA < M01420:85:000000000‑AC936:1:2101:15212:25690/51‑1 (MQ=60)
GGAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATA < M01420:85:000000000‑AC936:1:2104:15862:16363/51‑1 (MQ=60)
GAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAA < M01420:85:000000000‑AC936:1:1112:15284:13401/51‑1 (MQ=60)
GAACATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATA > M01420:85:000000000‑AC936:1:2101:19770:10541/1‑50 (MQ=60)
ATTCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGC > M01420:85:000000000‑AC936:1:1109:22227:27057/1‑50 (MQ=60)
TCAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAG < M01420:85:000000000‑AC936:1:1103:22248:8151/50‑1 (MQ=60)
CAAGCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCG < M01420:85:000000000‑AC936:1:1101:20764:12285/51‑1 (MQ=60)
GCAAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGT > M01420:85:000000000‑AC936:1:2106:5561:9966/1‑51 (MQ=60)
AAAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTT < M01420:85:000000000‑AC936:1:2101:3774:15358/51‑1 (MQ=60)
AAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTA < M01420:85:000000000‑AC936:1:2112:10940:18038/51‑1 (MQ=60)
AAAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTT > M01420:85:000000000‑AC936:1:1106:22038:24792/1‑50 (MQ=60)
AAGCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTAC < M01420:85:000000000‑AC936:1:2103:22218:13033/51‑1 (MQ=60)
GCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGG < M01420:85:000000000‑AC936:1:2101:20822:19419/51‑1 (MQ=60)
GCCTGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGG < M01420:85:000000000‑AC936:1:2102:13882:10858/51‑1 (MQ=60)
TGGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATT > M01420:85:000000000‑AC936:1:1113:24724:20510/1‑51 (MQ=60)
GGTTCCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGAT < M01420:85:000000000‑AC936:1:1105:10515:11402/49‑1 (MQ=60)
CCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCC < M01420:85:000000000‑AC936:1:2104:16576:5811/50‑1 (MQ=60)
CCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCC < M01420:85:000000000‑AC936:1:2112:8652:5111/50‑1 (MQ=60)
CCTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCC < M01420:85:000000000‑AC936:1:2114:17501:14602/50‑1 (MQ=60)
CTCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCT > M01420:85:000000000‑AC936:1:2112:15198:19455/1‑51 (MQ=60)
|
GCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCT > NC_017635/3020279‑3020378
|
| 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: ‑ |
