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 |
|
A2 F5 I181 R1
|
159 |
32.7 |
1279082 |
96.9% |
1239430 |
121.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
557,194 |
A→G |
Q681R (CAG→CGG) |
sfmD → |
fimbrial biogenesis usher protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 557,194 | 0 | A | G | 100.0%
| 110.6
/ NA
| 30 | Q681R (CAG→CGG) | sfmD | fimbrial biogenesis usher protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/13); total (17/13) |
GGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGT > NZ_CP009273/557079‑557291
|
ggTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGgt < 2:75560/129‑1 (MQ=255)
ggTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGgt > 1:75560/1‑129 (MQ=255)
ggTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCT‑GGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCa > 1:452659/1‑139 (MQ=255)
tACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGa > 2:151130/1‑138 (MQ=255)
cGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATgg > 1:334656/1‑139 (MQ=255)
cGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATgg > 2:134346/1‑139 (MQ=255)
cacGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCT‑GGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcc < 2:452659/139‑1 (MQ=255)
acGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcc < 1:285821/139‑1 (MQ=255)
cGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcca < 1:484037/139‑1 (MQ=255)
gggCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagccag > 2:395593/1‑139 (MQ=255)
cAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCt > 2:23952/1‑139 (MQ=255)
gcgcCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCtt > 2:59436/1‑138 (MQ=255)
gcgcCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCtt > 2:5749/1‑138 (MQ=255)
cTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcg < 2:334656/139‑1 (MQ=255)
gggggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcgc < 1:23952/137‑1 (MQ=255)
ggggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCa > 2:80325/1‑81 (MQ=255)
ggggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCa < 1:80325/81‑1 (MQ=255)
cGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGgt > 1:394344/1‑139 (MQ=255)
ggTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGaaaa < 2:343889/70‑1 (MQ=255)
ggTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGaaaa > 1:343889/1‑70 (MQ=255)
gTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGgt > 1:578125/1‑52 (MQ=255)
gTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGgt < 2:578125/52‑1 (MQ=255)
ataACTACGACCGCGATCAACATGACGTTAACTGGCGGCt < 2:137675/40‑1 (MQ=255)
ataACTACGACCGCGATCAACATGACGTTAACTGGCGGCt > 1:137675/1‑40 (MQ=255)
aCCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAg > 2:260277/1‑120 (MQ=255)
aCCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAg < 1:260277/120‑1 (MQ=255)
cGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAgg > 2:309168/1‑105 (MQ=255)
cGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAgg < 1:309168/105‑1 (MQ=255)
aCTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcgc < 1:620684/97‑1 (MQ=255)
aCTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcgc > 2:620684/1‑97 (MQ=255)
|
GGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGT > NZ_CP009273/557079‑557291
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCTATGCGG > NZ_CP009273/557068‑557343
|
ACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGC > SRR3722135.76589/1‑150 (MQ=60)
ACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCT‑GGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCAT > SRR3722135.458781/1‑151 (MQ=60)
GGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGC > SRR3722135.339410/1‑151 (MQ=60)
cgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGC < SRR3722135.81409/103‑1 (MQ=60)
CACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGG < SRR3722135.289923/151‑1 (MQ=60)
ACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGG < SRR3722135.490536/151‑1 (MQ=60)
ACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTG > SRR3722135.399829/1‑151 (MQ=60)
GCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtctt > SRR3722135.348764/1‑92 (MQ=60)
CTGGGGGGCGGGCATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCActgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaacaaaacaa > SRR3722135.585741/1‑74 (MQ=60)
cgtgggctcggagatgtgtataagagacagACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTAC < SRR3722135.628813/119‑1 (MQ=60)
aagagacaGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGC < SRR3722135.263981/143‑1 (MQ=60)
GGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGctgtctcttatacacatctccgagcccacgagaccgtactagatatcgtatgccgtcttctgcttgaaaaaaaaaaaaacacgaaatc > SRR3722135.139572/1‑62 (MQ=60)
GGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTAC < SRR3722135.24257/149‑1 (MQ=60)
cggagatgtgtataagagacagGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCA < SRR3722135.313593/127‑1 (MQ=60)
CGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCTATGCGG < SRR3722135.5830/151‑1 (MQ=60)
CGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCTATGCGG < SRR3722135.597943/151‑1 (MQ=60)
CGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCTATGCGG < SRR3722135.60228/151‑1 (MQ=60)
|
ACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCTATGCGG > NZ_CP009273/557068‑557343
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
