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 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	858,772	T→C	I66V (ATT→GTT)	ybiY ←	glycyl‑radical enzyme activating protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	858,772	0	T	C	100.0%	114.9 / NA	32	I66V (ATT→GTT)	ybiY	glycyl‑radical enzyme activating protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/19); total (13/19)

CTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTA  >  NZ_CP009273/858647‑858902

ctcAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGgcg                                                                                                                         <  2:208275/137‑1 (MQ=255)

                    cacacaCGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCa                                                                                                   <  1:445851/139‑1 (MQ=255)

                             ttAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTc                                                                                             >  1:19673/1‑136 (MQ=255)

                                aTGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGaca                                                                                       <  1:514689/139‑1 (MQ=255)

                                     tgtgTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCt                                                                                                                   >  2:418878/1‑106 (MQ=255)

                                     tgtgTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCt                                                                                                                   <  1:418878/106‑1 (MQ=255)

                                       tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACtt                                                                                                                               <  1:132220/92‑1 (MQ=255)

                                       tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACtt                                                                                                                               >  2:132220/1‑92 (MQ=255)

                                       tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTc                                                                                  <  2:391947/137‑1 (MQ=255)

                                       tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  1:308176/1‑139 (MQ=255)

                                       tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  1:485939/1‑139 (MQ=255)

                                       tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  2:266048/1‑139 (MQ=255)

                                         tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  2:419164/138‑1 (MQ=255)

                                         tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  1:463726/138‑1 (MQ=255)

                                         tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCAGTCAGCGCGCGCTCAACCACGTCCGGCGCGGCCGTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  2:112023/138‑1 (MQ=255)

                                           ggACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCg                                                                             <  1:305111/138‑1 (MQ=255)

                                              cagcagTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCAt                                                                         <  1:292580/139‑1 (MQ=255)

                                                 cagTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               >  2:282782/1‑130 (MQ=255)

                                                 cagTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  1:47583/130‑1 (MQ=255)

                                                 cagTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  1:282782/130‑1 (MQ=255)

                                                 cagTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               >  2:47583/1‑130 (MQ=255)

                                                            cGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCtgc                                                           >  2:150441/1‑139 (MQ=255)

                                                                           cGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCtt                                            >  2:205044/1‑139 (MQ=255)

                                                                                   aCTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATAcagca                                                                   <  2:524468/108‑1 (MQ=255)

                                                                                   aCTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATAcagca                                                                   >  1:524468/1‑108 (MQ=255)

                                                                                                            aTTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCGAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGaa           <  1:345366/139‑1 (MQ=255)

                                                                                                            aTTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGaa           <  2:405087/139‑1 (MQ=255)

                                                                                                              tCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGaa           >  2:419418/1‑137 (MQ=255)

                                                                                                                     gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGcgcg                                                >  2:108721/1‑93 (MQ=255)

                                                                                                                     gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGcgcg                                                <  1:108721/93‑1 (MQ=255)

                                                                                                                     gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTa  <  2:308176/139‑1 (MQ=255)

                                                                                                                     gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTa  <  1:205044/139‑1 (MQ=255)

CTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTA  >  NZ_CP009273/858647‑858902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCGCAGAACGGTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTAAGAAATACGAC  >  NZ_CP009273/858623‑858913

GCGCAGAACGGTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACC                                                                                                                                              >  SRR3722139.267282/1‑151 (MQ=60)

          GTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCG                                                                                                                                    <  SRR3722139.402164/151‑1 (MQ=60)

               acggtctcgtgggctcggagatgtgtataagagacaGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCC                                                                                                                               <  SRR3722139.133834/115‑1 (MQ=60)

                            cggagatgtgtataagagacagCGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGC                                                                                                                   <  SRR3722139.423833/128‑1 (MQ=60)

                                          ACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCC                                                                                                       >  SRR3722139.19866/1‑148 (MQ=60)

                                           CCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGAC                                                                                                   <  SRR3722139.451085/151‑1 (MQ=60)

                                                    GTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTG                                                                                          >  SRR3722139.311991/1‑151 (MQ=60)

                                                    GTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTG                                                                                          >  SRR3722139.491597/1‑151 (MQ=60)

                                                       AATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGT                                                                                       <  SRR3722139.520606/151‑1 (MQ=60)

                                                                GTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGC                                                                               <  SRR3722139.286341/150‑1 (MQ=60)

                                                                GTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGC                                                                               <  SRR3722139.469153/150‑1 (MQ=60)

                                                                GTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGC                                                                               <  SRR3722139.48136/150‑1 (MQ=60)

                                                                  CGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAG                                                                             <  SRR3722139.308894/150‑1 (MQ=60)

                                                                     ACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCC                                                                         <  SRR3722139.296255/151‑1 (MQ=60)

                                                                                              cggtctcgtgggctcggagatgtgtataagagacagCCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGAGCCTGCGTGCGGGCGCGGCTTTCCGGGT                                                <  SRR3722139.110051/115‑1 (MQ=60)

                                                                                                CTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCtgtctcttatacacatctcc                                              >  SRR3722139.530513/1‑131 (MQ=60)

                                                                                                                                   CATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCGAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTAAG           <  SRR3722139.349555/151‑1 (MQ=60)

                                                                                                                                            CGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTAAGAAATACGAC  <  SRR3722139.207581/151‑1 (MQ=60)

GCGCAGAACGGTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTAAGAAATACGAC  >  NZ_CP009273/858623‑858913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`