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 |
|
A2 F12 I1 R1
|
58 |
76.7 |
3263832 |
98.3% |
3208346 |
146.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,684,230 |
+CGGG |
intergenic (‑133/+71) |
PP_4986 ← / ← PP_4987 |
hemolysin III family channel protein/putative Chemotaxis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,684,230 | 1 | . | C | 100.0%
| 37.6
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (1/12); total (1/12) |
| * | NC_002947_CJ‑RC | 5,684,230 | 2 | . | G | 100.0%
| 39.0
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/12); total (1/12) |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 100.0%
| 38.0
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/12); total (1/12) |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 100.0%
| 38.7
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/12); total (1/12) |
ACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTT > NC_002947_CJ‑RC/5684086‑5684344
||||
aCCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccggg > 2:257253/1‑145 (MQ=255)
aCCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccgg < 6:370474/148‑4 (MQ=255)
aCCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccg < 7:171682/147‑3 (MQ=255)
gTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccggggc < 8:300290/148‑7 (MQ=255)
aaaCACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGcc < 6:325511/149‑1 (MQ=38)
aaCACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGTGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGccc < 3:148947/149‑1 (MQ=38)
aGACCTCCTGAGGTGGGGTGTGTTCCTGTTGTGACGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGATGCGGACCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATc < 8:360579/148‑1 (MQ=37)
gACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCTAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATcgc < 1:353690/149‑1 (MQ=37)
ctcctGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGac < 3:281218/149‑1 (MQ=37)
aGGTGGGCTGGGTTCCTGTTGTGATGCTGTTGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAg < 2:40916/148‑1 (MQ=25)
aGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACaa < 3:197848/147‑1 (MQ=37)
ggTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGTCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACaa < 7:303850/146‑1 (MQ=37)
ggTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACaa < 7:29671/146‑1 (MQ=37)
ggTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACaa < 7:96364/146‑1 (MQ=37)
gTGGGCTGGGTTCCTGTTGTGTTGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGc < 1:352113/148‑1 (MQ=25)
gCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCCGCCCTATAGCGCCACAAGGCCGCGCCCACACCAGACCACCCCGCCCGGCGCCGCACATACAAAACAAgg > 8:142460/1‑146 (MQ=18)
cccAGGCTTTCATTCCCACAGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCttt < 3:7744/149‑1 (MQ=38)
||||
ACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTT > NC_002947_CJ‑RC/5684086‑5684344
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTC > NC_002947_CJ‑RC/5684084‑5684345
|
TCACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcgg < NB501016:282:H2V7GAFX2:4:11605:3738:19064/150‑4 (MQ=60)
CATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCA < NB501016:282:H2V7GAFX2:1:21109:24798:6191/151‑1 (MQ=60)
CATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCCTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcggggggggggggcc > NB501016:282:H2V7GAFX2:3:11611:8595:15199/1‑136 (MQ=60)
GCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCC < NB501016:282:H2V7GAFX2:4:11504:8145:16008/151‑1 (MQ=60)
AAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGTGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCT < NB501016:282:H2V7GAFX2:2:11303:22112:3965/151‑1 (MQ=60)
AGACCTCCTGCGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCTAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCG < NB501016:282:H2V7GAFX2:1:21303:16654:2601/151‑1 (MQ=60)
CCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACA < NB501016:282:H2V7GAFX2:2:21203:14022:16162/151‑1 (MQ=60)
GAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGTCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAG < NB501016:282:H2V7GAFX2:4:21504:4000:13118/149‑1 (MQ=60)
GAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAG < NB501016:282:H2V7GAFX2:2:11311:13144:3655/149‑1 (MQ=60)
GAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAG < NB501016:282:H2V7GAFX2:4:11405:19973:19185/149‑1 (MQ=60)
GAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAG < NB501016:282:H2V7GAFX2:4:11504:14983:19475/149‑1 (MQ=60)
GGTGGGCTGGGTTCCTGTTGTGTTGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCC < NB501016:282:H2V7GAFX2:1:21302:5179:12422/150‑1 (MQ=60)
CGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcggggggggggggggggcccatagcggcccaagggcccgcccccacccccccccccaccccgcggccgcccacccaaaacaaaggaaggtttgagatacg > NB501016:282:H2V7GAFX2:2:11211:4556:2442/1‑51 (MQ=60)
AAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcgggggggggggggggcccggaagcggcccaacgccgcgccccccccccaccccccccccccgcgcccgcccgacgaaacaaaggcaggggggggttgagcg > NB501016:282:H2V7GAFX2:1:21101:16323:2762/1‑49 (MQ=60)
CCCCAGGCTTTCATTCCCACAGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTC < NB501016:282:H2V7GAFX2:2:11102:10486:8814/151‑1 (MQ=60)
CACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTT < NB501016:282:H2V7GAFX2:3:11407:22959:13569/106‑1 (MQ=60)
|
TCACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTC > NC_002947_CJ‑RC/5684084‑5684345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
