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
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
507,425 |
+A |
coding (27/564 nt) |
h16_B0448 → |
fragment of ABC‑type transport system,periplasmic component: APC family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 507,423 | 1 | . | A | 100.0%
| 93.3
/ NA
| 25 | E9K (GAA→AAA) | h16_B0448 | fragment of ABC‑type transport system,periplasmic component: APC family |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (12/13); total (12/13) |
TTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGGCCGATGTCGGGCGC > AM260480/507300‑507542
|
ttGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAAt > 2:894887/1‑134 (MQ=255)
gcgTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCgcgcttca < 1:890537/134‑4 (MQ=255)
cgTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCgcgctggcg < 1:670888/134‑1 (MQ=255)
ttCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGATGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCgcgctggcgct > 2:602273/1‑134 (MQ=255)
ccgccTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTc < 2:976961/134‑1 (MQ=255)
cATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGgc > 1:509807/1‑134 (MQ=255)
tGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGATGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGgcgc < 1:602273/134‑1 (MQ=255)
tGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGgcgc < 1:489903/134‑1 (MQ=255)
tGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGgcgc < 2:509807/134‑1 (MQ=255)
tCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑aaac < 2:324725/64‑3 (MQ=255)
tCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑aaac > 1:324725/1‑62 (MQ=255)
cGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCg > 1:1063408/1‑134 (MQ=255)
cGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCg > 1:287055/1‑134 (MQ=255)
ggCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTc < 2:1063408/134‑1 (MQ=255)
ggCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTc < 2:87253/134‑1 (MQ=255)
accacATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTg < 1:894887/134‑1 (MQ=255)
tAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCt > 2:1047730/1‑126 (MQ=255)
tAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCt < 1:1047730/126‑1 (MQ=255)
gTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTg < 1:65102/124‑1 (MQ=255)
gTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTg > 2:65102/1‑124 (MQ=255)
ccTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCggg < 2:287055/134‑1 (MQ=255)
gACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGcc < 2:532048/80‑1 (MQ=255)
gACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGcc > 1:532048/1‑80 (MQ=255)
gACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGcc > 2:660465/1‑134 (MQ=255)
aCGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCg > 1:290081/1‑134 (MQ=255)
ggCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCg > 1:499917/1‑134 (MQ=255)
aCGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGGCCGATGTCGGgcgc > 1:1072675/1‑134 (MQ=255)
|
TTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGGCCGATGTCGGGCGC > AM260480/507300‑507542
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ 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
ACTGGGCGAACTGGAGACATCGTTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGGCCGATGTCGGGCGCGACCAATACGATGGCTTTCTGCTTGCCGTTG > AM260480/507278‑507573
|
ACTGGGCGAACTGGAGACATCGTTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AAac < GWNJ‑0478:712:GW2002102894th:2:2204:17652:57480/150‑3 (MQ=60)
ACTGGGCGAACTGGAGACATCGTTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AAac < GWNJ‑0478:712:GW2002102894th:2:1204:19462:61420/150‑3 (MQ=60)
ttttttcttttatattgtttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcgggatgtgtataagagacagCCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AAac < GWNJ‑0478:712:GW2002102894th:2:1102:7942:39390/52‑3 (MQ=60)
atacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAA < GWNJ‑0478:712:GW2002102894th:2:1211:2720:53995/99‑1 (MQ=60)
GCGAACTGGAGACATCGTTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAA < GWNJ‑0478:712:GW2002102894th:2:1214:10010:2750/150‑1 (MQ=60)
GGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTtcaggaagactcccgatt < GWNJ‑0478:712:GW2002102894th:2:2203:4580:32345/150‑19 (MQ=60)
GCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCG > GWNJ‑0478:712:GW2002102894th:2:1212:8939:50763/1‑150 (MQ=60)
GCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCG < GWNJ‑0478:712:GW2002102894th:2:2107:11712:47394/150‑1 (MQ=60)
tttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:1206:21186:25251/69‑1 (MQ=60)
ATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGATGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAG < GWNJ‑0478:712:GW2002102894th:2:2103:9324:24114/150‑1 (MQ=60)
ATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAG < GWNJ‑0478:712:GW2002102894th:2:1213:6627:53364/150‑1 (MQ=60)
tttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtggggctcggagatgtgtataagagacagaAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAG < GWNJ‑0478:712:GW2002102894th:2:2107:15325:84712/66‑1 (MQ=60)
CCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAActgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgt > GWNJ‑0478:712:GW2002102894th:2:1202:6332:37905/1‑94 (MQ=60)
GTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGG > GWNJ‑0478:712:GW2002102894th:2:2212:11096:17840/1‑150 (MQ=60)
GTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGG > GWNJ‑0478:712:GW2002102894th:2:1201:14709:2603/1‑150 (MQ=60)
gacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCA < GWNJ‑0478:712:GW2002102894th:2:2216:16220:48970/94‑1 (MQ=60)
GGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGG < GWNJ‑0478:712:GW2002102894th:2:2210:1382:34611/150‑1 (MQ=60)
CACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGC < GWNJ‑0478:712:GW2002102894th:2:1104:12248:6867/150‑1 (MQ=60)
CACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGC < GWNJ‑0478:712:GW2002102894th:2:2203:19742:59385/150‑1 (MQ=60)
CCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCctgtctcttatacacatctccgagcccacgagacactcgc > GWNJ‑0478:712:GW2002102894th:2:1215:2564:57591/1‑110 (MQ=60)
CACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGT > GWNJ‑0478:712:GW2002102894th:2:1201:9771:22197/1‑150 (MQ=60)
ATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGG > GWNJ‑0478:712:GW2002102894th:2:1213:14909:100036/1‑150 (MQ=60)
GGCAATGACAATTCGACGGAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGGCCGATGTCGGGCGCG > GWNJ‑0478:712:GW2002102894th:2:2212:14305:64941/1‑150 (MQ=60)
GAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCtgtctcttatacacatctccgagcccacgagacactcg > GWNJ‑0478:712:GW2002102894th:2:2208:12932:10838/1‑112 (MQ=60)
GAGGAGACATGAAACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCtgtctcttatacacatctccgagcccacgagacactcg > GWNJ‑0478:712:GW2002102894th:2:1211:18400:18742/1‑112 (MQ=60)
ACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2201:14214:65438/1‑70 (MQ=60)
|
ACTGGGCGAACTGGAGACATCGTTGCAGTAGGGCAATACCACGGGCGGCGTTCGCCGCCTGACATGGGGAGCCGTTCAGGCTCGCGTCCGCACGGGCACCACATAGAGTGCCTGACGGGCAATGACAATTCGACGGAGGAGACATG‑AACAGAAATGCGTGGCAATCGCCGCCGCGCTGGCGCTGCTCGCGCCGGCGCTGGCCAGTGCTGAAGTGAAGGTCGGCATTCTTGCCACCCTTTCGGGGCCGTCGGCCGATGTCGGGCGCGACCAATACGATGGCTTTCTGCTTGCCGTTG > AM260480/507278‑507573
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
