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
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
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%
| 109.6
/ NA
| 26 | coding (203/1221 nt) | h16_A2693 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (13/13); total (13/13) |
CTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCC > AM260479/2907210‑2907442
|
cTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTAc < 1:898926/134‑1 (MQ=255)
gccgccGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCt > 2:924090/1‑134 (MQ=255)
gccgccGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCt > 1:757676/1‑134 (MQ=255)
ccgccgGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTg < 1:191909/134‑1 (MQ=255)
cACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACg < 1:169776/134‑1 (MQ=255)
gctgctCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTg > 2:925306/1‑106 (MQ=255)
gctgctCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTg < 1:925306/106‑1 (MQ=255)
ccGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGcc < 2:405601/134‑1 (MQ=255)
acacCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCgg > 1:945560/1‑134 (MQ=255)
gagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcggc > 2:796408/1‑134 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 1:178533/1‑91 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 2:178533/91‑1 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTcgc < 1:11432/83‑1 (MQ=255)
agctTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTcgc > 2:11432/1‑83 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGaa < 2:985803/54‑1 (MQ=19)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGaa > 1:985803/1‑54 (MQ=19)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 2:25169/1‑73 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 1:25169/73‑1 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCt < 1:913945/108‑1 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCt > 2:913945/1‑108 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGcc > 2:257430/1‑121 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGcc < 1:257430/121‑1 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCt < 2:310689/122‑1 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCt > 1:310689/1‑122 (MQ=255)
ggAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAgg < 1:924090/131‑1 (MQ=255)
tcaagaaCAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGccc > 2:655661/6‑134 (MQ=255)
|
CTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCC > AM260479/2907210‑2907442
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
CAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCAC > AM260479/2907197‑2907446
|
ggttccgtgGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTG > GWNJ‑0478:712:GW2002102894th:2:2116:18998:45646/10‑150 (MQ=60)
agatgtagctccgtctcgtgggctcggagatgtgtataagagacagCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:1108:7394:7974/104‑1 (MQ=60)
GCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCC < GWNJ‑0478:712:GW2002102894th:2:2208:16312:60580/150‑1 (MQ=60)
GCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAAC < GWNJ‑0478:712:GW2002102894th:2:1112:13636:32593/150‑1 (MQ=60)
gtataagagacagGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAAC < GWNJ‑0478:712:GW2002102894th:2:2210:9941:18655/136‑1 (MQ=60)
CCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGC < GWNJ‑0478:712:GW2002102894th:2:1110:14613:99641/150‑1 (MQ=60)
gagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:1103:18786:74729/103‑1 (MQ=60)
ccgtctcgtgggctcggagatgtgtataagagacAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGC < GWNJ‑0478:712:GW2002102894th:2:1101:12063:82268/115‑1 (MQ=60)
GCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGC > GWNJ‑0478:712:GW2002102894th:2:2212:18185:38482/1‑150 (MQ=60)
CAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCctgtctcttatacacatctccgagcccac > GWNJ‑0478:712:GW2002102894th:2:1113:6072:52496/1‑121 (MQ=60)
ataagagacagGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTC < GWNJ‑0478:712:GW2002102894th:2:2211:19492:51654/138‑1 (MQ=60)
GTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:2214:8455:65945/1‑84 (MQ=60)
GTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGC > GWNJ‑0478:712:GW2002102894th:2:1205:20663:95239/1‑150 (MQ=60)
ACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCC < GWNJ‑0478:712:GW2002102894th:2:1201:9304:35418/149‑1 (MQ=60)
GGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCAC < GWNJ‑0478:712:GW2002102894th:2:2210:4280:11554/147‑1 (MQ=60)
|
CAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCAC > AM260479/2907197‑2907446
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
