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 |
2,907,329 |
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%
| 86.4
/ NA
| 20 | coding (203/1221 nt) | h16_A2693 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (9/11); total (9/11) |
GCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACC > AM260479/2907194‑2907447
|
gcgcAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCCgg > 2:235580/1‑134 (MQ=255)
aaCCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 1:177228/134‑1 (MQ=255)
aaCCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 1:937494/134‑1 (MQ=255)
ctgctCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGt > 1:317922/1‑134 (MQ=255)
ggagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcgg < 2:499535/134‑1 (MQ=255)
ggagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcgg < 2:317922/134‑1 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGt > 1:103107/1‑134 (MQ=255)
cGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGcc < 1:272188/133‑1 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 2:972993/78‑1 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 1:972993/1‑78 (MQ=255)
tCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAg > 2:402974/1‑134 (MQ=255)
tcaagaaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGc > 2:323252/6‑109 (MQ=255)
tcaagaaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGc < 1:323252/104‑1 (MQ=255)
agaaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGcc < 2:270318/82‑1 (MQ=255)
agaaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGcc > 1:270318/3‑84 (MQ=255)
agaaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCa > 1:940210/3‑134 (MQ=255)
aaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCAcc < 1:402974/134‑1 (MQ=255)
tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGc < 1:33732/58‑1 (MQ=38)
tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGc > 2:33732/1‑58 (MQ=38)
tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGgcggcg > 1:676445/1‑90 (MQ=255)
tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGgcggcg < 2:676445/90‑1 (MQ=255)
|
GCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACC > AM260479/2907194‑2907447
|
| 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCGGCACCTCTGCCGGGGG > AM260479/2907201‑2907477
|
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:1114:9875:80928/150‑1 (MQ=60)
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:1205:11180:39402/150‑1 (MQ=60)
agtgaatttttttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGAC < GWNJ‑0478:712:GW2002102894th:2:1211:4592:73228/53‑1 (MQ=53)
GCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTG > GWNJ‑0478:712:GW2002102894th:2:1204:14699:31401/1‑150 (MQ=60)
GAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:1113:10808:45317/150‑1 (MQ=60)
GAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2210:2695:58858/150‑1 (MQ=60)
cagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagatcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCC < GWNJ‑0478:712:GW2002102894th:2:1105:20517:35267/82‑1 (MQ=60)
CAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTC > GWNJ‑0478:712:GW2002102894th:2:1106:19576:97194/1‑150 (MQ=60)
GAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCctgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:2213:17953:61951/1‑108 (MQ=60)
ataagagacagGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGC < GWNJ‑0478:712:GW2002102894th:2:1204:19225:66548/139‑1 (MQ=60)
GTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1210:18293:72434/1‑71 (MQ=42)
ACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCC < GWNJ‑0478:712:GW2002102894th:2:1203:17184:22317/149‑1 (MQ=60)
AGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2202:17775:2256/1‑66 (MQ=32)
TCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCtgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:1203:13078:7161/1‑115 (MQ=60)
TCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCAC > GWNJ‑0478:712:GW2002102894th:2:2210:9663:74677/1‑150 (MQ=60)
atcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCctgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2110:20353:43629/7‑120 (MQ=60)
GAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCGG < GWNJ‑0478:712:GW2002102894th:2:1211:9953:58655/150‑1 (MQ=60)
GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCtgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:2106:14581:37813/1‑110 (MQ=60)
|
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCGGCACCTCTGCCGGGGG > AM260479/2907201‑2907477
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
