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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
510,152 |
Δ1 bp |
coding (164/459 nt) |
ybbJ ← |
NfeD family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 510,151 | 0 | C | . | 95.0%
| 72.9
/ ‑2.8
| 20 | coding (165/459 nt) | ybbJ | NfeD family protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (9/10); total (9/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAA > NZ_CP009273/510064‑510226
|
gtgCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGcac > 1:1321611/1‑88 (MQ=255)
gtgCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGcac > 1:235100/1‑88 (MQ=255)
gcgACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCAccagcca > 1:114635/1‑90 (MQ=255)
cAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGacc > 2:263955/1‑90 (MQ=255)
ccATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGaccacc < 1:20742/90‑1 (MQ=255)
ttCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCCCCAGGc < 1:232467/90‑1 (MQ=255)
caccacAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCgg < 2:198321/90‑1 (MQ=255)
gCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCAc > 1:763064/1‑90 (MQ=255)
ccAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCAcc < 2:114635/90‑1 (MQ=255)
aGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGaccacc > 2:628568/1‑73 (MQ=255)
aGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGaccacc < 1:628568/73‑1 (MQ=255)
gcgAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCa > 1:1290008/1‑90 (MQ=255)
gAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCAcg > 2:1117431/1‑90 (MQ=255)
agcagcGTCAGGATGGCAAACATTCCCCCTTGCC‑CTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCAcgc < 1:1312301/90‑1 (MQ=255)
gcagcGTCAGGATGGCAACCATTCCCCCTTG‑CACCCCCAACCCAGCGGCCCCAGCCAGACCCCCAGGCCGGTAATCACCGCTGCCAcgcc < 1:924643/90‑1 (MQ=255)
aGGATGGCAAACATTCCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCcaca < 2:32617/90‑1 (MQ=255)
aGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCcaca > 2:1246284/1‑90 (MQ=255)
ggATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCAcgcc > 1:327629/1‑81 (MQ=255)
ggATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCAcgcc < 2:327629/81‑1 (MQ=255)
ggATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCacaa < 1:654045/90‑1 (MQ=255)
ggCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACaaa > 1:298553/1‑90 (MQ=255)
aaaCATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATaa < 2:235100/90‑1 (MQ=255)
|
GTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAA > NZ_CP009273/510064‑510226
|
| 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
CTATCGCTGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGG > NZ_CP009273/510056‑510248
|
ttttcgttttttttttgtcccccccCCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTC < SRR3722078.157170/75‑1 (MQ=60)
tgtttttttttcccccccCCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTGCCCCTTG‑CACTCCCAACCC < SRR3722078.556529/82‑1 (MQ=60)
tgtttTTTTGTCCGCGCCCCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCC < SRR3722078.1278468/95‑1 (MQ=60)
CGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCA > SRR3722078.115978/1‑100 (MQ=60)
gagacagCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAA < SRR3722078.635799/93‑1 (MQ=60)
CCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAA < SRR3722078.21003/100‑1 (MQ=60)
tgcctccactgcccggcgcCGAGCAGGGTCAGGATGGCAAACATTCCCCCTTG‑CACTCCCAACCCAACGGCACCAGCCAGACCACCAGGCCGGTAATCAC < SRR3722078.1478779/81‑1 (MQ=60)
TTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCCCCAGGCCGGTAATCAC < SRR3722078.235284/100‑1 (MQ=60)
TTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCAC > SRR3722078.772879/1‑100 (MQ=60)
cgcccgccatcgtcggcagcgtcagatgtgtataagagacagTTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACC < SRR3722078.1445447/58‑1 (MQ=60)
CAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCA > SRR3722078.1310540/1‑100 (MQ=60)
AGCAGCGTCAGGATGGCAAACATTCCCCCTTGCC‑CTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAA < SRR3722078.1333261/100‑1 (MQ=60)
AGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAA > SRR3722078.331647/1‑100 (MQ=60)
GCAGCGTCAGGATGGCAACCATTCCCCCTTG‑CACCCCCAACCCAGCGGCCCCAGCCAGACCCCCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAAC < SRR3722078.937322/100‑1 (MQ=60)
GCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAA > SRR3722078.302206/1‑100 (MQ=60)
GGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCA < SRR3722078.661540/100‑1 (MQ=60)
ACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAActgtctcttatacaca > SRR3722078.546919/1‑84 (MQ=60)
CATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCA > SRR3722078.849941/1‑100 (MQ=60)
CATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCA > SRR3722078.1347221/1‑100 (MQ=60)
TTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGC > SRR3722078.523914/1‑100 (MQ=60)
CCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT > SRR3722078.378446/1‑100 (MQ=60)
CCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT > SRR3722078.244138/1‑100 (MQ=60)
TTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGG > SRR3722078.1528893/1‑100 (MQ=60)
|
CTATCGCTGTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCTCGG > NZ_CP009273/510056‑510248
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
