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 F2 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,726,562 |
(T)5→4 |
coding (971/2574 nt) |
clpB ← |
ATP‑dependent chaperone ClpB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,726,558 | 0 | T | . | 79.2%
| 45.5
/ 20.8
| 24 | coding (975/2574 nt) | clpB | ATP‑dependent chaperone ClpB |
| Reads supporting (aligned to +/- strand): ref base T (2/3); new base . (10/9); total (12/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCAT > NZ_CP009273/2726470‑2726641
|
cTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCtt > 1:720220/1‑90 (MQ=255)
aCGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTAc < 1:237880/90‑1 (MQ=255)
aCGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTAc > 2:204283/1‑90 (MQ=255)
aTCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGc > 2:571199/1‑90 (MQ=255)
aTCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGc > 2:517732/1‑90 (MQ=255)
cAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGcgtcg > 2:552923/1‑90 (MQ=255)
cAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGcgtcgt > 2:68021/1‑90 (MQ=255)
cAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGcgtcgt > 2:543306/1‑90 (MQ=255)
aaCAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTg < 1:67023/90‑1 (MQ=255)
aaCAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTg < 2:377587/90‑1 (MQ=255)
cAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGc < 1:72946/90‑1 (MQ=255)
gAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCAc > 2:197398/1‑90 (MQ=255)
aaGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCAcc < 1:277904/90‑1 (MQ=255)
aaGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCAcc < 1:68021/90‑1 (MQ=255)
aGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCt > 2:299894/1‑90 (MQ=255)
cTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACg > 1:377748/1‑90 (MQ=255)
cGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGc < 1:519494/90‑1 (MQ=255)
cGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCa > 2:766360/1‑90 (MQ=255)
gCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGt < 1:77732/90‑1 (MQ=255)
tCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTcaccac > 2:461847/1‑90 (MQ=255)
acgacgTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAgc > 1:415114/1‑90 (MQ=255)
acgTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAgcgc < 2:715115/90‑1 (MQ=255)
acgTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCACTGCAATTCACCACGCGCCAgcgc < 1:552923/90‑1 (MQ=255)
acgTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGcc < 2:508406/90‑1 (MQ=255)
cagcaTC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCAt < 2:377748/90‑1 (MQ=255)
|
CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCAT > NZ_CP009273/2726470‑2726641
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATT > NZ_CP009273/2726468‑2726657
|
agagacagGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGT < SRR3722079.198123/92‑1 (MQ=60)
ACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATT < SRR3722079.239884/100‑1 (MQ=60)
CAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACG > SRR3722079.380814/1‑100 (MQ=60)
AACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGC < SRR3722079.67572/100‑1 (MQ=60)
CAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAG < SRR3722079.73552/100‑1 (MQ=60)
AAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGC < SRR3722079.280223/100‑1 (MQ=60)
AAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGC < SRR3722079.68580/100‑1 (MQ=60)
CGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTC < SRR3722079.524284/100‑1 (MQ=60)
GCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACC < SRR3722079.78366/100‑1 (MQ=60)
CTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGC > SRR3722079.418679/1‑100 (MQ=60)
ACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCACTGCAATTCACCACGCGCCAGCGCCGGTTTCAGC < SRR3722079.558233/100‑1 (MQ=60)
CTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATT > SRR3722079.828386/1‑100 (MQ=60)
|
TTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATT > NZ_CP009273/2726468‑2726657
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
