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
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,515,314 |
Δ1 bp |
intergenic (+253/‑570) |
tRNA‑Pro (CGG) → / → pilB |
tRNA‑Pro/Type IV pilus assembly protein PilB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,515,314 | 0 | G | . | 100.0%
| 86.1
/ NA
| 20 | intergenic (+253/‑570) | tRNA‑Pro (CGG)/pilB | tRNA‑Pro/Type IV pilus assembly protein PilB |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (11/9); total (11/9) |
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGG > AM260479/3515214‑3515437
|
ctactGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGc > 2:649157/1‑131 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTc > 1:478280/1‑109 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTc < 2:478280/109‑1 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCtt > 1:1148768/1‑133 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCtt > 2:402963/1‑133 (MQ=255)
gcACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGccc < 2:1148768/134‑1 (MQ=255)
cACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTc > 2:665126/1‑108 (MQ=255)
cACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTc < 1:665126/108‑1 (MQ=255)
aTTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATc > 1:246968/1‑134 (MQ=255)
ggCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTg < 1:649157/133‑1 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGt < 2:287012/56‑1 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGt > 2:386428/1‑56 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGt < 1:386428/56‑1 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGt > 1:287012/1‑56 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGAc > 1:763840/1‑129 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGAc < 2:763840/129‑1 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑cct > 2:682270/1‑132 (MQ=255)
tGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAgg < 1:682270/134‑1 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTg < 1:825139/113‑1 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTg > 2:825139/1‑113 (MQ=255)
|
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGG > AM260479/3515214‑3515437
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ 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
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATG > AM260479/3515214‑3515452
|
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTgtctcttat > GWNJ‑0478:712:GW2002102894th:2:1213:17609:40283/1‑141 (MQ=60)
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTG > GWNJ‑0478:712:GW2002102894th:2:2216:5207:14303/1‑149 (MQ=60)
agcagaagacggcatacgagcttagcgagtgtctcgtgggctcggagatgtgtataagagacAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAG < GWNJ‑0478:712:GW2002102894th:2:1206:4058:38042/88‑1 (MQ=60)
ataagagacagGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGC < GWNJ‑0478:712:GW2002102894th:2:2107:16134:55283/138‑1 (MQ=60)
TTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCT > GWNJ‑0478:712:GW2002102894th:2:1114:8744:15631/1‑150 (MQ=60)
GTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgct > GWNJ‑0478:712:GW2002102894th:2:1201:20193:18985/1‑87 (MQ=60)
GTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑Cctt > GWNJ‑0478:712:GW2002102894th:2:2110:14026:93945/1‑147 (MQ=60)
gagacaGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATC < GWNJ‑0478:712:GW2002102894th:2:2115:7455:91994/144‑1 (MQ=60)
CGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATC < GWNJ‑0478:712:GW2002102894th:2:2104:18279:62924/149‑1 (MQ=60)
GTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATG < GWNJ‑0478:712:GW2002102894th:2:2106:12691:56634/150‑1 (MQ=60)
|
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATG > AM260479/3515214‑3515452
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
