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 |
3,529,607 |
+C |
intergenic (‑121/‑183) |
secA ← / → h16_A3265 |
preprotein translocase subunit SecA/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,529,606 | 1 | . | C | 100.0%
| 106.0
/ NA
| 28 | intergenic (‑120/‑184) | secA/h16_A3265 | preprotein translocase subunit SecA/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (15/13); total (15/13) |
GCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGC > AM260479/3529475‑3529730
|
gCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCAcgg‑c < 1:242266/134‑1 (MQ=255)
gTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCAcgg‑ccgg > 2:532624/1‑130 (MQ=255)
cgGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAggg < 1:532624/134‑1 (MQ=255)
gggCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGggcaggc > 1:1115868/1‑132 (MQ=255)
gggATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGt < 2:1115868/133‑1 (MQ=255)
ctgctCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGc > 2:543727/1‑89 (MQ=255)
ctgctCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGc < 1:543727/89‑1 (MQ=255)
ctgctCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCAcgcg > 1:202312/1‑134 (MQ=255)
cggcggCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGt > 1:575152/1‑134 (MQ=255)
cggcCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCg > 2:358454/1‑134 (MQ=255)
cGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCGGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCAc > 1:421826/1‑114 (MQ=255)
cGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCGGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCAc < 2:421826/114‑1 (MQ=255)
cgcAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGAtt > 1:603077/1‑113 (MQ=255)
cgcAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGAtt < 2:603077/113‑1 (MQ=255)
aaaCGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAggg > 1:219602/1‑64 (MQ=255)
aaaCGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAggg < 2:219602/64‑1 (MQ=255)
aaCGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCAt > 1:401499/1‑134 (MQ=255)
aCGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCAtt < 2:202312/134‑1 (MQ=255)
cGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTg < 1:358454/134‑1 (MQ=255)
cGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTg > 2:171945/1‑115 (MQ=255)
cGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGAAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTg < 1:171945/115‑1 (MQ=255)
ggggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGt < 1:224128/61‑1 (MQ=255)
ggggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGt > 2:224128/1‑61 (MQ=255)
ggggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCAt > 1:48349/1‑112 (MQ=255)
ggggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCAt < 2:48349/112‑1 (MQ=255)
ggggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTgggg < 1:826130/128‑1 (MQ=255)
ggggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTgggg > 2:826130/1‑128 (MQ=255)
gggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGggc > 2:116335/1‑41 (MQ=255)
gggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGggc < 1:116335/41‑1 (MQ=255)
gggTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGgccgc > 2:1078585/1‑134 (MQ=255)
|
GCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGC > AM260479/3529475‑3529730
|
| 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
GACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGCCGCAGCTTCAATCCACAGTCGGGC > AM260479/3529460‑3529754
|
cactgcgtctgtgttccttgttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtatgagagacagGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CC < GWNJ‑0478:712:GW2002102894th:2:1211:5876:15208/50‑1 (MQ=60)
GGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGC < GWNJ‑0478:712:GW2002102894th:2:1115:3030:87062/150‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagccccagGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGG < GWNJ‑0478:712:GW2002102894th:2:1214:14512:44123/113‑1 (MQ=60)
CACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCA > GWNJ‑0478:712:GW2002102894th:2:2215:16369:71445/1‑148 (MQ=60)
GCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCC < GWNJ‑0478:712:GW2002102894th:2:1215:6438:91935/150‑1 (MQ=60)
tttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGG < GWNJ‑0478:712:GW2002102894th:2:1108:11241:16442/71‑1 (MQ=60)
CCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGT > GWNJ‑0478:712:GW2002102894th:2:1113:3463:82607/1‑150 (MQ=60)
aagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGG < GWNJ‑0478:712:GW2002102894th:2:1112:18172:95575/92‑1 (MQ=60)
GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTC > GWNJ‑0478:712:GW2002102894th:2:2101:7577:9524/1‑150 (MQ=60)
GCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCGGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGctgtct > GWNJ‑0478:712:GW2002102894th:2:1209:4213:32818/1‑144 (MQ=60)
agcgagtgtctcgtgggctcggagatgtgtataagagacagCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCC < GWNJ‑0478:712:GW2002102894th:2:2205:20153:10191/109‑1 (MQ=60)
GGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑Ccctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaatcccacccctt > GWNJ‑0478:712:GW2002102894th:2:2209:20487:20889/1‑59 (MQ=60)
GAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCtgtctc > GWNJ‑0478:712:GW2002102894th:2:2103:15244:88698/1‑144 (MQ=60)
GGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCttgcctgcccctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgt > GWNJ‑0478:712:GW2002102894th:2:1112:17812:72816/1‑84 (MQ=60)
GATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATT > GWNJ‑0478:712:GW2002102894th:2:1208:21157:22535/1‑150 (MQ=60)
gacagGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGAAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGC < GWNJ‑0478:712:GW2002102894th:2:1110:1933:23427/145‑1 (MQ=60)
ACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGC < GWNJ‑0478:712:GW2002102894th:2:1204:3797:74306/150‑1 (MQ=60)
GAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCActgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaactaatgacccatggagtcgct > GWNJ‑0478:712:GW2002102894th:2:2208:5198:76842/1‑53 (MQ=60)
AGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGctgtctct > GWNJ‑0478:712:GW2002102894th:2:1102:6478:5481/1‑142 (MQ=60)
ATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGCCGCAGCTT < GWNJ‑0478:712:GW2002102894th:2:2114:5400:51305/150‑1 (MQ=60)
CGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGCCGCAGCTTCAATCCtgtctctt > GWNJ‑0478:712:GW2002102894th:2:2204:7760:96172/1‑142 (MQ=60)
GC‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGCCGCAGCTTCAATCCACAGTCGGGC > GWNJ‑0478:712:GW2002102894th:2:2208:9242:22806/1‑150 (MQ=60)
|
GACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTCCGCAGATTGCCCGCGTGATTGCCCGTGCGCCCATTGGCCACAGTTTGGGGCGGCCGCCGCAGCTTCAATCCACAGTCGGGC > AM260479/3529460‑3529754
|
| 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: ‑ |
