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
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
2,907,305 |
2 bp→AT |
coding (181‑182/1221 nt) |
h16_A2693 → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,907,305 | 0 | G | A | 100.0%
| 29.1
/ NA
| 9 | D61I (GAC→ATC) | h16_A2693 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (5/4); total (5/4) |
| * | AM260479 | 2,907,306 | 0 | A | T | 100.0%
| 28.4
/ NA
| 9 | D61I (GAC→ATC) | h16_A2693 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (5/4); total (5/4) |
CGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGG > AM260479/2907205‑2907410
||
gcatgatGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAgg > 2:1063896/7‑134 (MQ=255)
ccGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGcc < 1:1063896/134‑1 (MQ=255)
cAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTg > 1:857340/1‑133 (MQ=255)
gTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGcc > 1:897847/1‑61 (MQ=255)
gTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGcc < 2:897847/61‑1 (MQ=255)
agctgagctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCt < 1:147822/61‑1 (MQ=255)
agctgagctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCt > 2:147822/1‑61 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcgg < 1:387886/118‑1 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcgg > 2:387886/1‑118 (MQ=255)
||
CGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGG > AM260479/2907205‑2907410
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ 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
CTCGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCAC > AM260479/2907173‑2907425
|
cctgttcttcctgttgattttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTA < GWNJ‑0478:712:GW2002102894th:2:1201:6252:73254/52‑1 (MQ=42)
CGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGC < GWNJ‑0478:712:GW2002102894th:2:1110:2907:21323/150‑1 (MQ=60)
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:2212:14867:36834/150‑1 (MQ=60)
aagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAA < GWNJ‑0478:712:GW2002102894th:2:1109:5113:99536/91‑1 (MQ=60)
CGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGG > GWNJ‑0478:712:GW2002102894th:2:2116:2234:43232/1‑149 (MQ=60)
GCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAG < GWNJ‑0478:712:GW2002102894th:2:2212:17354:18953/150‑1 (MQ=60)
TGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtc > GWNJ‑0478:712:GW2002102894th:2:2213:7895:49652/1‑93 (MQ=60)
GAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtctt > GWNJ‑0478:712:GW2002102894th:2:2203:6908:78940/1‑92 (MQ=60)
AGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCAC < GWNJ‑0478:712:GW2002102894th:2:1206:11216:46831/150‑1 (MQ=60)
|
CTCGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCAC > AM260479/2907173‑2907425
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
