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 |
| JC |
AM260479 |
3,403,046 |
(AGGTCTCGCAGGCCAT)1→2 |
coding (772/996 nt) |
phcA ← |
transcriptional regulator, LysR‑family |
|
| |
seq id |
position |
reads (cov) |
reads (cov) |
score |
skew |
freq |
annotation |
gene |
product |
| * |
? |
AM260479 |
3403023 = | 0 (0.000) | 17 (0.700) |
17/200 |
0.4 |
100% |
coding (795/996 nt) |
phcA |
transcriptional regulator, LysR‑family |
| ? | AM260479 |
= 3403038 |
0 (0.000) | coding (780/996 nt) |
phcA |
transcriptional regulator, LysR‑family |
AGCAGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ < AM260479/3403159‑3403023
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atggcctgCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCG < AM260479/3403038‑3402942
AGCAGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGC < 2:405713/134‑1
GCAGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCC > 2:688635/1‑134
GCAGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCC < 1:688635/134‑1
GCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGAC < 2:760412/120‑1
GCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGAC > 1:760412/1‑120
GGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTG > 2:1001957/1‑134
TACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCC < 1:270229/134‑1
ATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTC < 1:1570/134‑1
CGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGA < 2:606797/134‑1
CCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAG < 2:524082/89‑1
CCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAG > 1:524082/1‑89
GATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTG < 1:938899/116‑1
GATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTG > 2:938899/1‑116
ACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCA < 2:44155/134‑1
CGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCC < 1:99894/60‑1
CGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCC > 2:99894/1‑60
AAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCG < 1:9447/127‑1
AAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCG > 2:9447/1‑127
CTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCT < 1:806896/73‑1
CTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCT > 2:806896/1‑73
AGCAGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ < AM260479/3403159‑3403023
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atggcctgCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCG < AM260479/3403038‑3402942
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
| Reads not counted as support for junction |
|---|
| read_name Not counted due to insufficient overlap past the breakpoint. |
| read_name Not counted due to not crossing MOB target site duplication. |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAGCGCGTAGTCGAGCGGAATCAGCGACGGCGCCG > AM260479/3402927‑3403195
|
CGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcaggccatgtccttggtcagcg > GWNJ‑0478:712:GW2002102894th:2:1101:7840:70058/1‑120 (MQ=60)
gctttgatccttttttaaatgttttttttgtttttgtttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagaCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGAT < GWNJ‑0478:712:GW2002102894th:2:1213:15863:96018/38‑1 (MQ=60)
GTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGctgt > GWNJ‑0478:712:GW2002102894th:2:2210:18247:66774/1‑146 (MQ=60)
AACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcaggccatgtccttggtcctgtctcttatacacatctccgagcccacgagacggagctacatctc > GWNJ‑0478:712:GW2002102894th:2:2202:17090:34837/1‑77 (MQ=60)
ATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATG > GWNJ‑0478:712:GW2002102894th:2:1101:20848:13149/1‑150 (MQ=60)
cgtgggctcggagatgtgtataagagacagcttcaggccataggtctcgCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGT < GWNJ‑0478:712:GW2002102894th:2:2101:3900:40023/100‑1 (MQ=60)
GTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTAC > GWNJ‑0478:712:GW2002102894th:2:1203:18217:6367/1‑150 (MQ=60)
CGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGActgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttc > GWNJ‑0478:712:GW2002102894th:2:1106:18719:75924/1‑90 (MQ=60)
gccttcaggccataggtctcgCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCC < GWNJ‑0478:712:GW2002102894th:2:2116:2210:27272/129‑1 (MQ=60)
gccataggtctcgCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCT > GWNJ‑0478:712:GW2002102894th:2:2113:18266:15117/14‑150 (MQ=60)
GGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAActgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccg > GWNJ‑0478:712:GW2002102894th:2:2209:9306:94352/1‑95 (MQ=60)
TGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAGCGCGTAGTCGAGCGGAATCAGCGACGGCGCCG > GWNJ‑0478:712:GW2002102894th:2:2212:20092:51626/1‑150 (MQ=60)
|
CGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAGCGCGTAGTCGAGCGGAATCAGCGACGGCGCCG > AM260479/3402927‑3403195
|
| 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: ‑ |
