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
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
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 = | 2 (0.080) | 23 (1.010) |
20/200 |
0.2 |
94.2% |
coding (795/996 nt) |
phcA |
transcriptional regulator, LysR‑family |
| ? | AM260479 |
= 3403038 |
1 (0.040) | coding (780/996 nt) |
phcA |
transcriptional regulator, LysR‑family |
AGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ < AM260479/3403156‑3403023
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atggcctgCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCGATGCTGGTGTGGGCGCGCAACC < AM260479/3403038‑3402920
AGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTG > 2:314465/1‑134
GGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGA > 2:456406/1‑134
CTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACC > 1:912337/1‑133
ACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCT > 2:95393/1‑134
GGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTG < 1:343934/134‑1
GGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTG < 1:491800/134‑1
TACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCC < 2:912337/134‑1
TACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCC < 2:618779/134‑1
ATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTC < 1:314465/134‑1
CCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACAC > 2:744319/1‑134
GCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTG < 1:456406/133‑1
ACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCT > 1:233/1‑134
CACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAG < 2:233/130‑1
GTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACA > 2:767985/1‑134
TCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGG < 2:140548/82‑1
TCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGG > 1:140548/1‑82
AAGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCGATGCTGG < 1:95393/134‑1
AGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCC < 1:728357/55‑1
AGGACATGGCCTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCC > 2:728357/1‑55
CTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAA > 2:472609/1‑106
CTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAA < 1:472609/106‑1
CTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACC < 1:927726/68‑1
CTGCGAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACC > 2:927726/1‑68
GAGACCTATGGCCTGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCGATGCTGGTGTGGGCGCGCAACC < 1:744319/134‑1
TGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGA > 2:324821/1‑41
TGCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGA < 1:324821/41‑1
AGCGCGGGCTCAAGCGCAATGCGACGCTGACGGTACATTCATGGCGTGCCCAGGCCGAACTGGCCTCGCAGACCGACATGATCTTCACCGTCAATGCGCTGACCAAGGACATGGCCTGCGAGACCTATGGCCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ < AM260479/3403156‑3403023
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atggcctgCGAGACCTATGGCCTGAAGGCCTTCCCGCTGCCGTCGGAACTGAACACCATGCTCGGCCTGAACATGTTCTGGCACCGCAGCCGCAACACCCATCCGATGCTGGTGTGGGCGCGCAACC < AM260479/3403038‑3402920
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ 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
CCACCACCTGGCGGAACAGGTTGCGCGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAGCGCGTAGTCGAGCGGAATCAGCGACG > AM260479/3402902‑3403189
|
CCACCACCTGGCGGAACAGGTTGCGCGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtc < GWNJ‑0478:712:GW2002102894th:2:2204:12038:20465/150‑6 (MQ=60)
CCACCTGGCGGAACAGGTTGCGCGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcg > GWNJ‑0478:712:GW2002102894th:2:2114:21123:7289/1‑142 (MQ=60)
GGTTGCGCGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcaggccatgtccttg > GWNJ‑0478:712:GW2002102894th:2:1106:9114:50478/1‑127 (MQ=60)
AGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcaggccatgtccttggtcctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:1215:3075:28497/1‑110 (MQ=60)
ccgtctcgtgggctcggagatgtgtataagagacagGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGT < GWNJ‑0478:712:GW2002102894th:2:1111:8277:29889/112‑1 (MQ=60)
GTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCC > GWNJ‑0478:712:GW2002102894th:2:1212:1633:40894/1‑149 (MQ=60)
CAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTC < GWNJ‑0478:712:GW2002102894th:2:1101:6228:3504/150‑1 (MQ=60)
GTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcaggccatgtccttggtcctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatg > GWNJ‑0478:712:GW2002102894th:2:2211:9846:75941/1‑72 (MQ=60)
agaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGC < GWNJ‑0478:712:GW2002102894th:2:2214:16921:44177/89‑1 (MQ=60)
AGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaac > GWNJ‑0478:712:GW2002102894th:2:1204:6705:62428/1‑62 (MQ=60)
ATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATG > GWNJ‑0478:712:GW2002102894th:2:1205:4526:91478/1‑150 (MQ=60)
GTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCG > GWNJ‑0478:712:GW2002102894th:2:1214:3440:27019/1‑150 (MQ=60)
GTTCAGTTCCGACGGCAGCGGGAAGGCCTTCAGGCCATAGGTCTCGCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCG > GWNJ‑0478:712:GW2002102894th:2:1207:11114:85824/1‑150 (MQ=60)
GTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaaagcaaacaa > GWNJ‑0478:712:GW2002102894th:2:2203:7000:61130/1‑54 (MQ=60)
GTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATaggtctcgcaggccatgtccttggtcagcgcattgactgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgctt > GWNJ‑0478:712:GW2002102894th:2:2115:13820:21177/1‑49 (MQ=60)
gtagctccgtctcgtgggctcggagatgtgtataagagacagGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAG < GWNJ‑0478:712:GW2002102894th:2:2109:10416:33140/108‑1 (MQ=60)
aggtctcgCAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAG < GWNJ‑0478:712:GW2002102894th:2:2208:6685:85521/141‑1 (MQ=60)
GGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAGCGCGTAGTCG > GWNJ‑0478:712:GW2002102894th:2:1210:9485:38976/1‑149 (MQ=60)
CCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaa > GWNJ‑0478:712:GW2002102894th:2:2105:5452:7314/1‑79 (MQ=60)
CCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCagcctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:1102:9967:92293/1‑132 (MQ=60)
GGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAActgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaa > GWNJ‑0478:712:GW2002102894th:2:1102:9636:62350/1‑79 (MQ=60)
|
CCACCACCTGGCGGAACAGGTTGCGCGCCCACACCAGCATCGGATGGGTGTTGCGGCTGCGGTGCCAGAACATGTTCAGGCCGAGCATGGTGTTCAGTTCCGACGGCAGCGGGAAGGCCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATAGGTCTCGCAGGCCATGTCCTTGGTCAGCGCATTGACGGTGAAGATCATGTCGGTCTGCGAGGCCAGTTCGGCCTGGGCACGCCATGAATGTACCGTCAGCGTCGCATTGCGCTTGAGCCCGCGCTGCTGCAGCGCGTAGTCGAGCGGAATCAGCGACG > AM260479/3402902‑3403189
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
