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 |
1,464,365 |
Δ1 bp |
coding (49/552 nt) |
h16_A1354 → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,464,365 | 0 | A | . | 100.0%
| 123.2
/ NA
| 28 | coding (49/552 nt) | h16_A1354 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (16/12); total (16/12) |
GCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGC > AM260479/1464253‑1464492
|
gCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAc > 1:403139/1‑130 (MQ=255)
gCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAc < 2:403139/130‑1 (MQ=255)
acaATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCAtt > 1:808880/1‑134 (MQ=255)
tGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAcc > 2:758223/1‑109 (MQ=255)
tGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAcc < 1:758223/109‑1 (MQ=255)
tGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGc < 1:18480/123‑1 (MQ=255)
tGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGc > 2:18480/1‑123 (MQ=255)
gcgcCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGc > 1:48122/1‑133 (MQ=255)
cgcgCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTg > 1:779017/1‑134 (MQ=255)
cAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAg > 1:131608/1‑134 (MQ=255)
ggAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcg > 2:781416‑M1/1‑132 (MQ=255)
tGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGc < 2:472820/80‑1 (MQ=255)
tGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGc > 1:472820/1‑80 (MQ=255)
tGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggc < 2:48122‑M1/134‑13 (MQ=255)
cGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcg < 2:779017‑M1/134‑17 (MQ=255)
cTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCt < 2:590927/53‑1 (MQ=255)
cTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCt > 1:590927/1‑53 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAc < 2:658494/46‑1 (MQ=39)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAc > 1:658494/1‑46 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtac > 1:491925‑M1/1‑103 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGccgct < 1:586684/99‑1 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGccgct > 2:586684/1‑99 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccag < 2:146716‑M1/134‑34 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtac > 2:629468‑M1/1‑101 (MQ=255)
gCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagca < 2:808880‑M1/134‑38 (MQ=255)
cTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcac > 2:685341‑M1/1‑96 (MQ=255)
ggCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcatt < 1:629468‑M1/134‑45 (MQ=255)
gTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagc > 2:660099‑M1/1‑82 (MQ=255)
|
GCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGC > AM260479/1464253‑1464492
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCGATTTCGTGGGCGCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCT > AM260479/1464235‑1464499
|
cgtgggctcggagatgtgtataagagacagGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAC < GWNJ‑0478:712:GW2002102894th:2:2208:20257:22564/118‑1 (MQ=60)
GATTTCGTGGGCGCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGC > GWNJ‑0478:712:GW2002102894th:2:1211:1942:70636/1‑150 (MQ=60)
ataagagacaGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCA < GWNJ‑0478:712:GW2002102894th:2:2116:6256:49226/140‑1 (MQ=60)
GGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTG > GWNJ‑0478:712:GW2002102894th:2:2202:12271:89305/1‑150 (MQ=60)
CAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGC < GWNJ‑0478:712:GW2002102894th:2:1103:8773:30180/150‑1 (MQ=60)
GCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCA > GWNJ‑0478:712:GW2002102894th:2:1102:6841:28194/1‑149 (MQ=60)
GGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGC > GWNJ‑0478:712:GW2002102894th:2:2201:13593:89294/1‑150 (MQ=60)
gcacccattGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGG > GWNJ‑0478:712:GW2002102894th:2:1109:7455:69071/10‑150 (MQ=60)
ggagatgtgtataagagacaGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCT < GWNJ‑0478:712:GW2002102894th:2:2107:11581:2949/130‑1 (MQ=60)
TGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCctgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:1215:20609:62882/1‑110 (MQ=60)
ATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:2107:9074:30913/1‑83 (MQ=60)
CGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2111:16694:57471/1‑76 (MQ=60)
CGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACC > GWNJ‑0478:712:GW2002102894th:2:1214:10458:68008/1‑149 (MQ=60)
CCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaatacagtcaat > GWNJ‑0478:712:GW2002102894th:2:2214:16766:93126/1‑62 (MQ=60)
CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt < GWNJ‑0478:712:GW2002102894th:2:2115:5808:101192/150‑10 (MQ=60)
GGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggtgagccgccgaa < GWNJ‑0478:712:GW2002102894th:2:2108:11258:79792/150‑21 (MQ=60)
|
GGCGATTTCGTGGGCGCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCT > AM260479/1464235‑1464499
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
