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 |
2,739,096 |
T→C |
E61G (GAA→GGA) |
rimM ← |
ribosome maturation factor RimM |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,739,096 | 0 | T | C | 97.6%
| 127.3
/ ‑4.0
| 41 | E61G (GAA→GGA) | rimM | ribosome maturation factor RimM |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/21); total (19/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.74e-01 |
ATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGTGGAA > NZ_CP009273/2739014‑2739179
|
aTTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTg > 1:938024/1‑90 (MQ=255)
aTTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTg > 1:455512/1‑90 (MQ=255)
cGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGAc < 2:1309295/90‑1 (MQ=255)
cGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGAc > 2:63070/1‑90 (MQ=255)
agcagGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTtgc < 1:326911/90‑1 (MQ=255)
cgcATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGAcc < 2:146193/90‑1 (MQ=255)
cgcATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGAcc < 1:441978/90‑1 (MQ=255)
gcATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGAccc < 2:669173/90‑1 (MQ=255)
cATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCg < 2:1419759/90‑1 (MQ=255)
aCGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCtt < 1:1102891/90‑1 (MQ=255)
cGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTc < 1:391859/90‑1 (MQ=255)
cGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTc < 1:164563/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGAccc < 2:1552245/79‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGAccc > 1:1552245/1‑79 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 1:236671/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:1442649/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:1455354/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:664078/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 1:63070/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt > 2:343439/1‑90 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:537313/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATCATCATGTCCTGATTGTGGTGCTTCCATCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 1:694937/90‑1 (MQ=255)
tttCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAggg > 1:560783/1‑90 (MQ=255)
tttCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAggg > 1:991691/1‑90 (MQ=255)
tttCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAggg > 2:681104/1‑90 (MQ=255)
tgatgaTCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGt > 1:1063496/1‑90 (MQ=255)
tgatgaTCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGt > 1:447838/1‑90 (MQ=255)
ccTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTc < 2:1017080/56‑1 (MQ=255)
ccTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTc > 1:1017080/1‑56 (MQ=255)
gATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:1493200/58‑1 (MQ=255)
gATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt > 1:1493200/1‑58 (MQ=255)
gATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCgg > 1:34522/1‑90 (MQ=255)
gATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCgg > 2:603270/1‑90 (MQ=255)
gATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCgg > 1:1118322/1‑90 (MQ=255)
gtggtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTc > 2:1373308/1‑90 (MQ=255)
tggtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCg > 1:850569/1‑43 (MQ=255)
tggtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCg < 2:850569/43‑1 (MQ=255)
tggtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCt > 1:238588/1‑90 (MQ=255)
tggtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCt > 1:1468529/1‑90 (MQ=255)
gtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTc < 2:641461/90‑1 (MQ=255)
cTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGt < 2:1307063/90‑1 (MQ=255)
cagcttcccagctGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGTGgaa < 2:652473/90‑1 (MQ=255)
|
ATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGTGGAA > NZ_CP009273/2739014‑2739179
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GACAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGTGGAAGAAAACACTCTGAGC > NZ_CP009273/2739002‑2739194
|
GACAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGC < SRR3722078.591046/100‑1 (MQ=60)
CAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTG > SRR3722078.951034/1‑100 (MQ=60)
CAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTG > SRR3722078.460955/1‑100 (MQ=60)
AGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGAC < SRR3722078.330922/100‑1 (MQ=60)
CGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGG < SRR3722078.447277/100‑1 (MQ=60)
CATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAC > SRR3722078.1577523/1‑100 (MQ=60)
ACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAAC < SRR3722078.1119699/100‑1 (MQ=60)
CGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACC < SRR3722078.166480/100‑1 (MQ=60)
CGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACC < SRR3722078.396622/100‑1 (MQ=60)
CGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGG > SRR3722078.567375/1‑100 (MQ=60)
CGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGG > SRR3722078.1006099/1‑100 (MQ=60)
GTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGC < SRR3722078.63806/100‑1 (MQ=60)
GTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGC < SRR3722078.239557/100‑1 (MQ=60)
GTCAACGCCTTTCAGCTTGATCATCATGTCCTGATTGTGGTGCTTCCATCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGC < SRR3722078.703229/100‑1 (MQ=60)
CCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGT > SRR3722078.1079513/1‑100 (MQ=60)
CCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGT > SRR3722078.453197/1‑100 (MQ=60)
ATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCctgtctcttatacacatctgacgc > SRR3722078.1032090/1‑76 (MQ=60)
ATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCctgtctcttatacacatctgac > SRR3722078.1517546/1‑78 (MQ=60)
ATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGG > SRR3722078.34939/1‑100 (MQ=60)
ATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGG > SRR3722078.1135398/1‑100 (MQ=60)
GTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATctgtctcttatacacatctgacgctgccgacgatggc > SRR3722078.861927/1‑63 (MQ=60)
GTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCT > SRR3722078.241500/1‑100 (MQ=60)
GTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCT > SRR3722078.1492480/1‑100 (MQ=60)
TCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGTGGAAGAAAACACTCTGAGC > SRR3722078.139533/1‑100 (MQ=60)
|
GACAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGTGGAAGAAAACACTCTGAGC > NZ_CP009273/2739002‑2739194
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
