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
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
2,955,197 |
Δ1 bp |
coding (1034/1071 nt) |
h16_A2735 → |
phenylpropionate dioxygenase or related ring‑hydroxylating dioxygenase, large terminal subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,955,195 | 0 | C | . | 100.0%
| 87.3
/ NA
| 20 | coding (1032/1071 nt) | h16_A2735 | phenylpropionate dioxygenase or related ring‑hydroxylating dioxygenase, large terminal subunit |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (9/11); total (9/11) |
CGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGC > AM260479/2955063‑2955304
|
cGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAc < 1:80804/133‑1 (MQ=255)
aGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag < 1:894247/134‑3 (MQ=255)
gAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag < 2:473288/129‑3 (MQ=255)
gAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag > 1:473288/1‑127 (MQ=255)
gCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACgg < 1:148815/134‑1 (MQ=255)
gCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACgg < 1:220407/134‑1 (MQ=255)
cgccgcCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATgcag > 2:64958/1‑133 (MQ=255)
ccgccTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACgg > 1:1005902/1‑124 (MQ=255)
ccgccTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACgg < 2:1005902/124‑1 (MQ=255)
aTCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATcgccg < 2:322863/134‑1 (MQ=255)
cGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCcgcg > 1:246085/1‑134 (MQ=255)
agaTCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTAc > 1:322413/1‑134 (MQ=255)
gCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCg < 2:246085/133‑1 (MQ=255)
aCGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGt > 1:447715/1‑134 (MQ=255)
gCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTcc < 2:378306/134‑1 (MQ=255)
aTGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCcgg < 2:579459/134‑1 (MQ=255)
gATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGt > 1:363462/1‑127 (MQ=255)
gATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGt < 2:363462/127‑1 (MQ=255)
ccggcTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGc < 1:1001332/134‑1 (MQ=255)
cggcTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag > 2:321270/1‑46 (MQ=255)
cggcTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag < 1:321270/48‑3 (MQ=255)
gcTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTa > 1:739222/1‑87 (MQ=255)
gcTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTa < 2:739222/87‑1 (MQ=255)
ggCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAacgcacgc > 1:204868/1‑132 (MQ=255)
aCCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCt > 1:684567/1‑81 (MQ=255)
aCCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCt < 2:684567/81‑1 (MQ=255)
|
CGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGC > AM260479/2955063‑2955304
|
| 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
AATCGCGCTGTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCCCCTGGCGGTCCGTTT > AM260479/2955051‑2955333
|
AATCGCGCTGTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTC < GWNJ‑0478:712:GW2002102894th:2:1212:8093:55313/150‑1 (MQ=60)
GCGCTGTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCG > GWNJ‑0478:712:GW2002102894th:2:1215:6879:51028/1‑150 (MQ=60)
TCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAA < GWNJ‑0478:712:GW2002102894th:2:1107:3169:53861/149‑1 (MQ=60)
GAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGAC < GWNJ‑0478:712:GW2002102894th:2:2207:18478:96527/150‑1 (MQ=60)
tttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGAC < GWNJ‑0478:712:GW2002102894th:2:1204:9031:54032/78‑1 (MQ=60)
TCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATT > GWNJ‑0478:712:GW2002102894th:2:2215:4993:42750/1‑150 (MQ=60)
GGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCA < GWNJ‑0478:712:GW2002102894th:2:1111:16284:77890/150‑1 (MQ=60)
GGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCA < GWNJ‑0478:712:GW2002102894th:2:1115:17038:93328/150‑1 (MQ=60)
CATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGC > GWNJ‑0478:712:GW2002102894th:2:1116:19754:40590/1‑150 (MQ=60)
GCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACG > GWNJ‑0478:712:GW2002102894th:2:1204:7735:61490/1‑150 (MQ=60)
CGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTC > GWNJ‑0478:712:GW2002102894th:2:1212:13370:12529/1‑150 (MQ=60)
ATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGG > GWNJ‑0478:712:GW2002102894th:2:1208:4388:23808/1‑149 (MQ=60)
CATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCctgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2114:17391:4883/1‑117 (MQ=60)
GCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACG < GWNJ‑0478:712:GW2002102894th:2:2215:12844:17929/150‑1 (MQ=60)
GCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCA > GWNJ‑0478:712:GW2002102894th:2:1115:11632:6937/1‑148 (MQ=60)
cggagatgtgtataagagtcaGAAGTCGGGCCGTA‑CCATTCGCCGATGGAAGACGGCATGCAGCAGTTCCATGAGTGGTATCGCCGCGCCATGGCTTACTCCGGCTAGTCCTGCGGACTAGTGCTATAACCGCACAACGCACGCAAGAAC < GWNJ‑0478:712:GW2002102894th:2:2114:13674:31169/129‑1 (MQ=60)
CTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCctgtctcttatacacatctccgagcccacgagacggagc > GWNJ‑0478:712:GW2002102894th:2:2110:12476:91698/1‑111 (MQ=60)
AGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGctgtctcttatacacatctcc > GWNJ‑0478:712:GW2002102894th:2:2210:8579:8290/1‑129 (MQ=60)
AGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCCCCTGGCGGTCCGTTT > GWNJ‑0478:712:GW2002102894th:2:1116:4862:90182/1‑150 (MQ=60)
|
AATCGCGCTGTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCCCCTGGCGGTCCGTTT > AM260479/2955051‑2955333
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
