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 |
| RA |
AM260479 |
2,907,329 |
Δ1 bp |
coding (205/1221 nt) |
h16_A2693 → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,907,327 | 0 | G | . | 100.0%
| 51.9
/ NA
| 14 | coding (203/1221 nt) | h16_A2693 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (8/6); total (8/6) |
GCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGG > AM260479/2907248‑2907431
|
gCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCaa < 1:747058/113‑1 (MQ=255)
gCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCaa > 2:747058/1‑113 (MQ=255)
gagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGcc > 1:770886/1‑108 (MQ=255)
gagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGcc < 2:770886/108‑1 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAAATATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 1:303976/1‑91 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAAATATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 2:303976/91‑1 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCAcc > 1:462449/1‑134 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGc > 1:1030784/1‑83 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGc < 2:1030784/83‑1 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAgg > 1:33568/1‑134 (MQ=255)
tGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTa > 1:830875/1‑47 (MQ=12)
tGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTa < 2:830875/47‑1 (MQ=12)
tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 1:912888/48‑1 (MQ=37)
tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 2:912888/1‑48 (MQ=37)
|
GCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGG > AM260479/2907248‑2907431
|
| 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
TGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCC > AM260479/2907189‑2907442
|
agagacaggttcttgggcatgaTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGG < GWNJ‑0478:712:GW2002102894th:2:2116:8295:23172/128‑1 (MQ=60)
gagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:2213:6771:66332/103‑1 (MQ=60)
cctgcgcgggcaGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAAC < GWNJ‑0478:712:GW2002102894th:2:2211:9769:57262/138‑1 (MQ=60)
gagacaGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGT < GWNJ‑0478:712:GW2002102894th:2:2114:14751:22252/144‑1 (MQ=60)
tttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagatcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2208:7556:88937/72‑1 (MQ=60)
CCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtctt > GWNJ‑0478:712:GW2002102894th:2:1116:20207:67077/1‑91 (MQ=60)
CCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCtgtctcttat > GWNJ‑0478:712:GW2002102894th:2:2116:16690:57338/1‑139 (MQ=60)
CAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAAATATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCctgtctcttatacacatctccgagcccac > GWNJ‑0478:712:GW2002102894th:2:1205:4614:24433/1‑121 (MQ=60)
GAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCC > GWNJ‑0478:712:GW2002102894th:2:1212:7782:74366/1‑150 (MQ=60)
GTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCctgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:2216:13442:43221/1‑113 (MQ=60)
GTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGC > GWNJ‑0478:712:GW2002102894th:2:1105:14920:35728/1‑150 (MQ=60)
TACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2204:14764:68859/1‑78 (MQ=55)
gtctcgtgggctcggagatgtgtataagagacagGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCC < GWNJ‑0478:712:GW2002102894th:2:1203:20533:2783/116‑1 (MQ=60)
GAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCctgtctcttatacacatctccgagcccacgagacggagctacatct > GWNJ‑0478:712:GW2002102894th:2:2207:13926:8641/1‑104 (MQ=60)
GCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCtgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:1103:11048:91678/1‑108 (MQ=60)
|
TGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCC > AM260479/2907189‑2907442
|
| 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: ‑ |
