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
|
155 |
25.8 |
2285122 |
88.0% |
2010907 |
104.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
2,907,313 |
Δ1 bp |
coding (189/1221 nt) |
h16_A2693 → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,907,311 | 0 | A | . | 100.0%
| 72.9
/ NA
| 17 | coding (187/1221 nt) | h16_A2693 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (9/8); total (9/8) |
CCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGC > AM260479/2907213‑2907411
|
ccgccgGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCt < 1:536918/133‑1 (MQ=255)
cgtagtCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCgg > 1:533619/6‑134 (MQ=255)
gtCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 2:833084/122‑1 (MQ=255)
gtCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 1:833084/2‑123 (MQ=255)
gaggagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGc > 1:1125306/1‑53 (MQ=255)
gaggagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGc < 2:251675/53‑1 (MQ=255)
gaggagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGc < 2:1125306/53‑1 (MQ=255)
gaggagCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGc > 1:251675/1‑53 (MQ=255)
gagCAGTACGAGCTGAGCTTCTGGGAATCGATCGAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcggc > 2:912406/1‑134 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTg < 1:555887/103‑1 (MQ=255)
gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTg > 2:555887/1‑103 (MQ=255)
agctgagctTCTGGGAATCGATCAAG‑AACAGCAATTATGc > 1:34865/1‑40 (MQ=255)
agctgagctTCTGGGAATCGATCAAG‑AACAGCAATTATGc < 2:34865/40‑1 (MQ=255)
tCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCt > 1:306795/1‑109 (MQ=255)
tCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCt < 2:306795/109‑1 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc > 2:1062359/1‑73 (MQ=255)
cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc < 1:1062359/73‑1 (MQ=255)
|
CCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGC > AM260479/2907213‑2907411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ 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
CATGCTCGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCG > AM260479/2907169‑2907461
|
gcgagtgtctcgtgggctcggagatgtgtataagagacagGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAA < GWNJ‑0478:712:GW2002102894th:2:2109:14160:18627/110‑1 (MQ=60)
GCTCGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTA < GWNJ‑0478:712:GW2002102894th:2:1110:9275:43856/150‑1 (MQ=60)
GCTCGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTA < GWNJ‑0478:712:GW2002102894th:2:2213:3305:16372/150‑1 (MQ=60)
ggctcggagatgtgtataagagacaGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:2210:9759:10430/125‑1 (MQ=60)
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC < GWNJ‑0478:712:GW2002102894th:2:2215:14534:64105/150‑1 (MQ=60)
gtttatttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCC < GWNJ‑0478:712:GW2002102894th:2:2112:13863:41671/67‑1 (MQ=34)
GCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAA < GWNJ‑0478:712:GW2002102894th:2:1214:5917:12828/149‑1 (MQ=60)
ttttgtttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagtctgggaatcgatcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAA < GWNJ‑0478:712:GW2002102894th:2:1114:18029:84478/50‑1 (MQ=46)
gcttcaggtaggcctcgtagTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGT > GWNJ‑0478:712:GW2002102894th:2:1215:1437:96508/21‑150 (MQ=60)
caggtaggcctcgtagTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTG > GWNJ‑0478:712:GW2002102894th:2:2114:4839:86950/17‑150 (MQ=60)
gagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2213:3283:7477/103‑1 (MQ=60)
atgtgtataagagacagCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGccgctccagg < GWNJ‑0478:712:GW2002102894th:2:1216:14185:4308/133‑11 (MQ=60)
agcgagtgtctcgtgggctcggagatgtgtataagagacagGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAG < GWNJ‑0478:712:GW2002102894th:2:2202:11076:54007/109‑1 (MQ=60)
ATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCCGGcgactacgaggcctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:1114:10395:34887/1‑71 (MQ=60)
ATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCCGGcgactacgaggcctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:2216:9023:16464/1‑71 (MQ=60)
CCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCCGGcgactacgaggcctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1105:6730:22817/1‑58 (MQ=56)
GGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1112:15847:48419/1‑77 (MQ=53)
AGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCtgtctcttat > GWNJ‑0478:712:GW2002102894th:2:1203:11235:54862/1‑140 (MQ=60)
atcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaa > GWNJ‑0478:712:GW2002102894th:2:1214:3837:16521/7‑78 (MQ=60)
agAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCG > GWNJ‑0478:712:GW2002102894th:2:1113:17806:101256/3‑150 (MQ=60)
|
CATGCTCGCCGCCGCGCCGCTGCCCGCGCAGGCGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCG > AM260479/2907169‑2907461
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
