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
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
2,860,853 |
C→A |
R442S (AGG→AGT) |
qseE ← |
two component system sensor histidine kinase QseE/GlrK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 2,860,853 | 0 | C | A | 96.8%
| 113.5
/ NA
| 31 | R442S (AGG→AGT) | qseE | two component system sensor histidine kinase QseE/GlrK |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (18/12); total (18/13) |
| Fisher's exact test for biased strand distribution p-value = 4.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTCTCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCCCTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCCC > NC_017635/2860806‑2860894
|
ctctCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACt < 2:352231/50‑1 (MQ=255)
ctctCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACt < 1:1240905/50‑1 (MQ=255)
atcgtcgACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTg < 1:1207884/48‑1 (MQ=255)
cgtcgACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGc > 2:1051176/1‑49 (MQ=255)
gtcgACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGc < 1:795586/48‑1 (MQ=255)
gACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATg < 2:182942/49‑1 (MQ=255)
gACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATg < 1:1506563/49‑1 (MQ=255)
aCCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCt > 2:1404348/1‑50 (MQ=255)
ccAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCt > 1:2035649/1‑49 (MQ=255)
cAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTa < 1:875416/50‑1 (MQ=255)
aGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTaa > 1:1172961/1‑50 (MQ=255)
aGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTaa > 2:2039489/1‑50 (MQ=255)
tACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATcc < 1:1149090/50‑1 (MQ=255)
cAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATccc < 2:1961698/49‑1 (MQ=255)
tCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGAcc > 1:817530/1‑50 (MQ=255)
ccccTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCg > 1:642684/1‑50 (MQ=255)
ccTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCt < 1:1485786/50‑1 (MQ=255)
ccTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCt > 1:106749/1‑50 (MQ=255)
cTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTg > 1:1816308/1‑50 (MQ=255)
ttGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGc > 1:884006/1‑50 (MQ=255)
gCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGccc > 2:1442823/1‑50 (MQ=255)
gCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGccc > 1:1208717/1‑50 (MQ=255)
gCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGccc > 1:121866/1‑50 (MQ=255)
aTACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCtt < 1:1178461/50‑1 (MQ=255)
aCGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCa > 2:1056971/1‑50 (MQ=255)
ggCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCAcc < 2:1964380/50‑1 (MQ=255)
ggCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCAcc > 1:1235430/1‑50 (MQ=255)
gAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGcc > 1:546541/1‑50 (MQ=255)
gAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGcc > 2:222211/1‑50 (MQ=255)
aaTACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGccc > 2:48908/1‑50 (MQ=255)
aTACAATCCCTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGcccc < 2:790650/50‑1 (MQ=255)
|
CTCTCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCCCTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCCC > NC_017635/2860806‑2860894
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCTCTCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCCCTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCCCTTTTCGCTG > NC_017635/2860805‑2860903
|
GCTCTCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACT < M01420:85:000000000‑AC936:1:2103:26964:22834/51‑1 (MQ=60)
gaTCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTG < M01420:85:000000000‑AC936:1:2103:10950:12756/48‑1 (MQ=60)
CGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGC < M01420:85:000000000‑AC936:1:1111:8740:21474/49‑1 (MQ=60)
CGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATG < M01420:85:000000000‑AC936:1:2107:6487:13258/50‑1 (MQ=60)
CCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTA < M01420:85:000000000‑AC936:1:1112:23579:23673/51‑1 (MQ=60)
CCAGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTT > M01420:85:000000000‑AC936:1:2114:4713:13091/1‑50 (MQ=60)
AGATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAAT > M01420:85:000000000‑AC936:1:2102:20485:25138/1‑51 (MQ=60)
ATACAGTTCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCC < M01420:85:000000000‑AC936:1:2102:8518:17219/51‑1 (MQ=60)
TCCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCG > M01420:85:000000000‑AC936:1:1112:7724:4874/1‑51 (MQ=60)
CCCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGC > M01420:85:000000000‑AC936:1:1109:11017:19325/1‑51 (MQ=60)
CCCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCT < M01420:85:000000000‑AC936:1:2107:19296:6530/51‑1 (MQ=60)
CCTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTG > M01420:85:000000000‑AC936:1:1102:28370:13964/1‑51 (MQ=60)
CTTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGC > M01420:85:000000000‑AC936:1:2111:10189:16287/1‑51 (MQ=60)
TTGCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCC > M01420:85:000000000‑AC936:1:1112:18901:27652/1‑51 (MQ=60)
GCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCT > M01420:85:000000000‑AC936:1:1102:15389:18396/1‑51 (MQ=60)
GCATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCT > M01420:85:000000000‑AC936:1:2103:7303:12992/1‑51 (MQ=60)
CATACGGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTT < M01420:85:000000000‑AC936:1:2102:16833:28114/51‑1 (MQ=60)
GGCGAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCG > M01420:85:000000000‑AC936:1:2103:10684:21034/1‑51 (MQ=60)
GAATACAATCACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCC > M01420:85:000000000‑AC936:1:1108:18299:12464/1‑51 (MQ=60)
CACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCCCTTTTCGCT > M01420:85:000000000‑AC936:1:2113:9969:9312/1‑51 (MQ=60)
ACTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCCCTTTTCGCTG > M01420:85:000000000‑AC936:1:2103:28154:13595/1‑51 (MQ=60)
|
GCTCTCGTCGACCAGATACAGTTCCCCTTGCATACGGCGAATACAATCCCTGGCAATGCTTAATCCCAGACCGCTGCCCTTCACCGCCCCTTTTCGCTG > NC_017635/2860805‑2860903
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
