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 |
1,671,899 |
T→G |
T88P (ACG→CCG) |
pntA ← |
Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,671,899 | 0 | T | G | 97.6%
| 130.2
/ ‑3.7
| 41 | T88P (ACG→CCG) | pntA | Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (20/20); total (21/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.59e-01 |
CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTT > NZ_CP009273/1671816‑1671985
|
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 1:957016/1‑90 (MQ=255)
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 2:947248/1‑90 (MQ=255)
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 2:409268/1‑90 (MQ=255)
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc < 2:395663/90‑1 (MQ=255)
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 1:939623/1‑90 (MQ=255)
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 1:1506579/1‑90 (MQ=255)
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 1:1279930/1‑90 (MQ=255)
tCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAg > 1:1118445/1‑90 (MQ=255)
tCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAg < 1:1000235/90‑1 (MQ=255)
ccATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGAt > 2:335005/1‑90 (MQ=255)
ccATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGAt < 2:1498577/90‑1 (MQ=255)
ccATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGAt < 2:1084245/90‑1 (MQ=255)
aTCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc > 1:1207976/1‑90 (MQ=255)
cGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTa < 1:1490519/90‑1 (MQ=255)
ggTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTaa < 2:1507811/90‑1 (MQ=255)
acgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTTACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtc < 1:28997/90‑1 (MQ=255)
acgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtc > 1:585692/1‑90 (MQ=255)
gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat > 2:466720/1‑90 (MQ=255)
gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat > 2:1228103/1‑90 (MQ=255)
gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat > 2:1021948/1‑90 (MQ=255)
gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGCGTCCCAGGATTCAGTAACGCAATTtcat > 2:1031196/1‑90 (MQ=255)
cGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCTAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCatcatc > 2:518162/1‑90 (MQ=255)
cGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCatcatc > 1:1302204/1‑90 (MQ=255)
cGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCatcatc > 1:841596/1‑90 (MQ=255)
aTTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTg < 1:409268/90‑1 (MQ=255)
aTTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTg < 1:1031196/90‑1 (MQ=255)
tCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTc < 2:1506579/90‑1 (MQ=255)
ccGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCa < 1:379614/90‑1 (MQ=255)
ccGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCa < 1:1539427/90‑1 (MQ=255)
ggATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGa > 1:99712/1‑90 (MQ=255)
cAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTg < 2:939623/90‑1 (MQ=255)
ggCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc < 1:753864/90‑1 (MQ=255)
gATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCa < 2:1367622/90‑1 (MQ=255)
aTAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAg < 1:1196477/90‑1 (MQ=255)
aaCTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc > 2:1213418/1‑90 (MQ=255)
aaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc < 2:1412425/90‑1 (MQ=255)
tCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAt < 2:86851/90‑1 (MQ=255)
cACCAGCGGTGTTCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAtt > 1:1197824/1‑90 (MQ=255)
cACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAtt > 1:1213193/1‑90 (MQ=255)
aCCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTc < 2:338995/90‑1 (MQ=255)
gCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCtt < 1:518162/90‑1 (MQ=255)
|
CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTT > NZ_CP009273/1671816‑1671985
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ 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
GCACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAATTTC > NZ_CP009273/1671806‑1671995
|
GCACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCC > SRR3722078.1531145/1‑100 (MQ=60)
GCACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCC > SRR3722078.970547/1‑100 (MQ=60)
GCACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCC > SRR3722078.952666/1‑100 (MQ=60)
GCACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCC > SRR3722078.1300287/1‑100 (MQ=60)
ACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAG > SRR3722078.1135524/1‑100 (MQ=60)
atctccacgaccgccatcgtcggcagcgtcagatgtgtataagagacagAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGA < SRR3722078.82885/51‑1 (MQ=60)
AGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGA < SRR3722078.256774/100‑1 (MQ=60)
GAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGAT < SRR3722078.1007580/100‑1 (MQ=60)
GTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTC > SRR3722078.1226951/1‑100 (MQ=60)
TCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAA < SRR3722078.1014842/100‑1 (MQ=60)
CGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTC < SRR3722078.1514819/100‑1 (MQ=60)
CGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTC > SRR3722078.592514/1‑100 (MQ=60)
CGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATC > SRR3722078.852814/1‑100 (MQ=60)
CGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATC > SRR3722078.1322971/1‑100 (MQ=60)
ACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTTACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAAC < SRR3722078.29357/100‑1 (MQ=60)
CATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGA > SRR3722078.100886/1‑100 (MQ=60)
ATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAA < SRR3722078.414220/100‑1 (MQ=60)
ATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAA < SRR3722078.1046504/100‑1 (MQ=60)
CCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTC < SRR3722078.384249/100‑1 (MQ=60)
CCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTC < SRR3722078.1564524/100‑1 (MQ=60)
GGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGC < SRR3722078.763509/100‑1 (MQ=60)
AGATAAAACTCACCAGCGGTGTTCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATT > SRR3722078.1216611/1‑100 (MQ=60)
AGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATT > SRR3722078.1232263/1‑100 (MQ=60)
ATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCC < SRR3722078.1215244/100‑1 (MQ=60)
CACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCtgtctctt > SRR3722078.1066440/1‑92 (MQ=60)
CCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAGTCCCTTCTACAAT > SRR3722078.767044/1‑100 (MQ=60)
GCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAATTTC < SRR3722078.524295/100‑1 (MQ=60)
|
GCACAGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAATTTC > NZ_CP009273/1671806‑1671995
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
