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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,972,691 |
A→G |
intergenic (‑237/‑543) |
flhD ← / → uspC |
flagellar transcriptional regulator FlhD/universal stress protein UspC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,972,691 | 0 | A | G | 100.0%
| 84.7
/ NA
| 25 | intergenic (‑237/‑543) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/10); total (15/10) |
TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATAC > NZ_CP009273/1972605‑1972771
|
tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCT‑AATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑Ggggggg > 1:316141/1‑90 (MQ=255)
aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc < 1:675041/90‑1 (MQ=255)
tGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGAttt > 2:665267/1‑90 (MQ=255)
tCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCaa > 1:15593/1‑90 (MQ=255)
tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCaata > 1:506166/1‑90 (MQ=255)
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGA‑TTTCAATAATGCGTg > 1:617486/1‑90 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGTGGCGTTTTTCATTAATGCgga > 1:478468/1‑88 (MQ=255)
tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCggg > 2:448586/1‑88 (MQ=255)
tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATca < 2:566480/90‑1 (MQ=255)
ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcac > 1:277678/1‑90 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca > 2:738880/1‑90 (MQ=255)
ccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACaa < 2:416036/90‑1 (MQ=255)
aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAac < 2:118660/90‑1 (MQ=255)
gACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCa > 2:643553/1‑90 (MQ=255)
cGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt < 1:55170/90‑1 (MQ=255)
agCAACCGGACTCCTCCCCACCCGCAACTTCAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt < 2:478468/89‑1 (MQ=255)
gCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt < 1:738880/90‑1 (MQ=255)
cACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg > 1:611794‑M1/1‑82 (MQ=255)
cTACACGCATATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTa < 2:153727/75‑1 (MQ=255)
cTACACGCACATACAAC‑GGGTGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTa > 1:153727/1‑75 (MQ=255)
cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg > 2:740212‑M1/1‑80 (MQ=255)
cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > 2:83676‑M1/1‑73 (MQ=255)
caTACAAC‑GGGGGGGGGCTGCGA‑TTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc < 2:617486‑M1/90‑21 (MQ=255)
aTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc > 2:114532‑M1/1‑70 (MQ=255)
aTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaaca > 2:197127‑M1/1‑70 (MQ=255)
aTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaaca < 1:197127‑M1/84‑15 (MQ=255)
|
TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATAC > NZ_CP009273/1972605‑1972771
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGT > NZ_CP009273/1972595‑1972786
|
AATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCT‑AATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGG > SRR3722073.322840/1‑100 (MQ=60)
TAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAA > SRR3722073.15990/1‑100 (MQ=60)
AGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAAT < SRR3722073.688846/100‑1 (MQ=60)
GAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATA > SRR3722073.516850/1‑100 (MQ=60)
nnnnnnnnnnnnnnnnnnnntTAAGATTTTTCCTAAATCGACGCAACTGTACTNGTCACTANNCGCACANACAACGGGGGGGGGatgagattttannnna < SRR3722073.488720/79‑17 (MQ=60)
GGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGA‑TTTCAATAATGCGTG > SRR3722073.630320/1‑100 (MQ=60)
GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGtggcgtttttcattaatgcgga > SRR3722073.488651/1‑78 (MQ=60)
TATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCAC > SRR3722073.283557/1‑100 (MQ=60)
CGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgga < SRR3722073.56469/100‑4 (MQ=60)
GCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaa < SRR3722073.753842/100‑5 (MQ=60)
CTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg > SRR3722073.624530/1‑92 (MQ=60)
GTACTCGTCACTACACGCACATACAACGGGTGGGGGCTGCGATTTTCAATAATGCGTGATGCGGATCACACAAAACACTCAATTACTTAAggaagctggc > SRR3722073.156848/1‑90 (MQ=60)
ACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgat < SRR3722073.201076/100‑25 (MQ=60)
CATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGctgtctcttatacacatctgacgctgccgacgatatgcagtgtgtagatctcggt > SRR3722073.573976/1‑45 (MQ=60)
ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatg > SRR3722073.146723/1‑65 (MQ=60)
|
AATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGT > NZ_CP009273/1972595‑1972786
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
