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 |
3,475,701 |
T→C |
S352P (TCG→CCG) |
yheS → |
ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,475,701 | 0 | T | C | 80.8%
| 46.7
/ 7.7
| 26 | S352P (TCG→CCG) | yheS | ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (2/3); new base C (10/11); total (12/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01 |
GATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTC > NZ_CP009273/3475617‑3475787
|
gATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACa < 1:607150/90‑1 (MQ=255)
aTCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAt > 2:12053/1‑90 (MQ=255)
ttattCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCa > 1:452131/1‑90 (MQ=255)
tattCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCaa < 1:94061/90‑1 (MQ=255)
cgactcgaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGtt > 2:725282/1‑90 (MQ=255)
gactcgaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTa < 1:269380/90‑1 (MQ=255)
gactcgaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTa < 2:595287/90‑1 (MQ=255)
cgaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCg > 2:671992/1‑90 (MQ=255)
gAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGC‑GGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTgcg > 2:720618/1‑90 (MQ=255)
tGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAg < 2:365538/90‑1 (MQ=255)
gTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTc < 2:75600/90‑1 (MQ=255)
ggCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGt < 1:712864/90‑1 (MQ=255)
cgTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTgcgc > 2:401213/1‑73 (MQ=255)
cgTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTgcgc < 1:401213/73‑1 (MQ=255)
ttGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTc < 2:243456/90‑1 (MQ=255)
gTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGGGAAATTGGTCTGGCGaa > 2:602014/1‑90 (MQ=255)
ttAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGaaa < 2:660583/90‑1 (MQ=255)
ttAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGaaa < 1:839511/90‑1 (MQ=255)
gCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGt < 2:579258/65‑1 (MQ=255)
gCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGt > 1:579258/1‑65 (MQ=255)
gCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCa > 2:412008/1‑90 (MQ=255)
aaTGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCaaa > 1:831090/1‑90 (MQ=255)
aTGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAAc < 2:36911/90‑1 (MQ=255)
gcgGGTAAATCGACATTAATCAAACTGTTAGCCGGCGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGc > 2:528342/1‑90 (MQ=255)
gcgGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGAATCAAACTCGGc > 2:681081/1‑90 (MQ=255)
aaaCCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTc < 2:452131/90‑1 (MQ=255)
|
GATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTC > NZ_CP009273/3475617‑3475787
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ 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
TGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAAC > NZ_CP009273/3475613‑3475776
|
TGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATC < SRR3722079.570854/100‑1 (MQ=60)
GGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCA > SRR3722079.456089/1‑100 (MQ=60)
GATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAGTCAAAC < SRR3722079.613271/100‑1 (MQ=60)
TATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCC < SRR3722079.94801/100‑1 (MQ=60)
GACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAAC < SRR3722079.271635/100‑1 (MQ=60)
gagacagGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGG < SRR3722079.404598/93‑1 (MQ=60)
GGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTC < SRR3722079.720451/100‑1 (MQ=60)
CTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCctgtctcttatacac > SRR3722079.584992/1‑85 (MQ=60)
GTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAA > SRR3722079.839986/1‑100 (MQ=60)
TTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAAC < SRR3722079.848496/100‑1 (MQ=60)
|
TGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAAC > NZ_CP009273/3475613‑3475776
|
| 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: ‑ |
