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
|
155 |
25.8 |
2285122 |
88.0% |
2010907 |
104.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,515,428 |
+C |
intergenic (+367/‑456) |
tRNA‑Pro (CGG) → / → pilB |
tRNA‑Pro/Type IV pilus assembly protein PilB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,515,427 | 1 | . | C | 100.0%
| 80.7
/ NA
| 23 | intergenic (+366/‑457) | tRNA‑Pro (CGG)/pilB | tRNA‑Pro/Type IV pilus assembly protein PilB |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (11/12); total (11/12) |
GGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAT > AM260479/3515299‑3515549
|
ggcggTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑ccttca < 2:837569/134‑6 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtct < 1:21156/134‑1 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtct > 1:75911/1‑134 (MQ=255)
aaaGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATcc < 2:79320/134‑1 (MQ=255)
aaaGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATcc < 2:75911/134‑1 (MQ=255)
aaaGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCAACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATcc < 1:12309/134‑1 (MQ=255)
cGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCtt > 1:294014/1‑134 (MQ=255)
agaAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtcttc > 2:808984/1‑97 (MQ=255)
agaAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtcttc < 1:808984/97‑1 (MQ=255)
tCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGt > 1:697697/1‑101 (MQ=255)
tCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGt < 2:697697/101‑1 (MQ=255)
tCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAgg > 2:902353/1‑134 (MQ=255)
cTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTtgt < 1:902353/133‑1 (MQ=255)
tGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAgg > 1:590610/1‑134 (MQ=255)
tGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTg > 1:1041757/1‑134 (MQ=255)
cATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGAt < 2:570330/71‑1 (MQ=255)
cATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGAt > 1:570330/1‑71 (MQ=255)
cTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATccc > 2:174721/1‑48 (MQ=39)
cTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATccc < 1:174721/48‑1 (MQ=255)
cTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGc < 2:602372/124‑1 (MQ=255)
cTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGc > 1:602372/1‑124 (MQ=255)
cTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAt > 2:538076/1‑134 (MQ=255)
gCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCATGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAt < 2:294014/131‑1 (MQ=255)
gCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCa < 2:590610/130‑1 (MQ=255)
|
GGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAT > AM260479/3515299‑3515549
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGCACGCAC > AM260479/3515282‑3515570
|
attagcgagtgtctcgtgggctcggagatgtgtataagagacagGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑Cctt < GWNJ‑0478:712:GW2002102894th:2:1201:1812:47677/106‑4 (MQ=60)
CGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATC < GWNJ‑0478:712:GW2002102894th:2:1206:10710:58805/149‑1 (MQ=60)
CCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTT > GWNJ‑0478:712:GW2002102894th:2:1104:15002:78882/1‑150 (MQ=60)
AAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATG < GWNJ‑0478:712:GW2002102894th:2:1103:16952:38125/150‑1 (MQ=60)
cggagatgtgtataagagacagAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGT < GWNJ‑0478:712:GW2002102894th:2:2115:8653:66861/127‑1 (MQ=60)
GGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTC > GWNJ‑0478:712:GW2002102894th:2:1201:5121:74709/1‑150 (MQ=60)
CAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCAACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATC < GWNJ‑0478:712:GW2002102894th:2:1101:4757:80538/150‑1 (MQ=60)
tttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCC < GWNJ‑0478:712:GW2002102894th:2:1110:13672:38262/79‑1 (MQ=60)
TGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTctgtctcttatacacatct > GWNJ‑0478:712:GW2002102894th:2:2108:12344:72041/1‑131 (MQ=60)
CTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaa > GWNJ‑0478:712:GW2002102894th:2:2209:6485:11093/1‑81 (MQ=60)
GCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGA < GWNJ‑0478:712:GW2002102894th:2:2204:2922:5004/149‑1 (MQ=60)
GCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGG > GWNJ‑0478:712:GW2002102894th:2:2103:3704:10967/1‑150 (MQ=60)
AACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGC > GWNJ‑0478:712:GW2002102894th:2:2210:20783:99876/1‑150 (MQ=60)
GCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTgtctcttatacacatctccgagcccacgagacactcgctaaactcgt > GWNJ‑0478:712:GW2002102894th:2:1216:8753:79118/1‑103 (MQ=60)
CTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATC > GWNJ‑0478:712:GW2002102894th:2:2103:8433:84087/1‑150 (MQ=60)
TCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGC > GWNJ‑0478:712:GW2002102894th:2:2206:18336:32505/1‑150 (MQ=60)
GACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGCACGCAC < GWNJ‑0478:712:GW2002102894th:2:1214:18958:17825/149‑1 (MQ=60)
|
TATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGCACGCAC > AM260479/3515282‑3515570
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
