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 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

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%	120.4 / NA	32	I66V (ATT→GTT)	ybiY	glycyl‑radical enzyme activating protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/13); total (19/13)

CTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTA  >  NZ_CP009273/858644‑858902

ctcctcAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGgc                                                                                                                          >  2:844722/1‑139 (MQ=255)

   ctcAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGgcgc                                                                                                                        <  1:261061/138‑1 (MQ=255)

   ctcAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGgc                                                                                                                          <  1:254695/136‑1 (MQ=255)

        cGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCt                                                                                                                   >  1:45170/1‑138 (MQ=255)

             ttcacttcacCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAgcg                                                                                                              >  1:491501/1‑138 (MQ=255)

                acttcacCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGcac                                                                                                           <  2:482241/138‑1 (MQ=255)

                     accacACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCTCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCg                                                                                                     >  2:457220/1‑139 (MQ=255)

                       cacacaCGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGgcgc                                                                                                                        <  1:322992/118‑1 (MQ=255)

                       cacacaCGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGgcgc                                                                                                                        >  2:322992/1‑118 (MQ=255)

                               gTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTc                                                                                             >  2:267893/1‑137 (MQ=255)

                                   aTGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGaca                                                                                       <  1:457220/139‑1 (MQ=255)

                                        tgtgTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTc                                                                                  >  1:437883/1‑139 (MQ=255)

                                          tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  2:257447/1‑139 (MQ=255)

                                          tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  1:789445/1‑139 (MQ=255)

                                          tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  1:690529/1‑139 (MQ=255)

                                          tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  1:467253/1‑139 (MQ=255)

                                          tgtCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGt                                                                                >  1:34678/1‑139 (MQ=255)

                                            tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  1:207817/138‑1 (MQ=255)

                                            tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  2:556019/138‑1 (MQ=255)

                                            tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  1:787558/138‑1 (MQ=255)

                                            tCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTg                                                                               <  2:45170/138‑1 (MQ=255)

                                                  agcagTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATa                                                                        >  2:77325/1‑139 (MQ=255)

                                                      gTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATAcagc                                                                    <  2:467253/139‑1 (MQ=255)

                                                                                           tCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGa                                >  2:649681/1‑138 (MQ=255)

                                                                                                    aTAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCgg                       >  1:238924/1‑138 (MQ=255)

                                                                                                                  cAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAg        >  2:291007/1‑139 (MQ=255)

                                                                                                                       cgcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCtt    >  2:797544/1‑138 (MQ=255)

                                                                                                                        gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCa                                                                          >  1:557363/1‑67 (MQ=255)

                                                                                                                        gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCa                                                                          <  2:557363/67‑1 (MQ=255)

                                                                                                                        gcgcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTa  <  2:789445/139‑1 (MQ=255)

                                                                                                                          gcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACAcc                            <  1:257589/111‑1 (MQ=255)

                                                                                                                          gcTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACAcc                            >  2:257589/1‑111 (MQ=255)

CTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTA  >  NZ_CP009273/858644‑858902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `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

GCAGAACGGTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTAA  >  NZ_CP009273/858625‑858903

GCAGAACGGTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCAC                                                                                                                                  <  SRR3722120.584997/151‑1 (MQ=60)

                GATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTT                                                                                                                   >  SRR3722120.45716/1‑150 (MQ=60)

                    ataagagacagTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGC                                                                                                              <  SRR3722120.327647/140‑1 (MQ=60)

                     CCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGC                                                                                                              <  SRR3722120.264826/150‑1 (MQ=60)

                     CCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGC                                                                                                              >  SRR3722120.498578/1‑150 (MQ=60)

                     CCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGC                                                                                                                <  SRR3722120.258385/148‑1 (MQ=60)

                                                CGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCG                                                                                  >  SRR3722120.444289/1‑151 (MQ=60)

                                                  GTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTG                                                                                >  SRR3722120.800074/1‑151 (MQ=60)

                                                  GTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTG                                                                                >  SRR3722120.699968/1‑151 (MQ=60)

                                                  GTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTG                                                                                >  SRR3722120.474028/1‑151 (MQ=60)

                                                  GTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTG                                                                                >  SRR3722120.35096/1‑151 (MQ=60)

                                                     AATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGT                                                                             <  SRR3722120.463865/151‑1 (MQ=60)

                                                              GTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGC                                                                     <  SRR3722120.798162/150‑1 (MQ=60)

                                                              GTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGC                                                                     <  SRR3722120.210685/150‑1 (MQ=60)

                                                                                                            TTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGC                       >  SRR3722120.242322/1‑150 (MQ=60)

                                                                                                                gatgtgtataagagacagATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCC                  <  SRR3722120.261319/133‑1 (MQ=60)

                                                                                                                                CCATTCAGCGCGCGCTCAACCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGtctcttatacacatctccgagcccacgagactaaggcgaatatcgtatgccgtcttctg  >  SRR3722120.565183/1‑92 (MQ=60)

GCAGAACGGTCGTCATGATCTCCTCAACGCTTTTCACTTCACCACACACGGTTAATGCCTGTGTCGGACAGCAGTCGGTTAACGCCGTCAGATGCTCCGGGGTTAACTTTTCCCGATGAATAAGCAAACCATTCAGCGCGCGCTCAATCACTTCCGGCGCGGCCTTAGCGCACAGCTCGCAGCCTTCCAGACACAGTCGTGCGTCATACAGCAGATCCTGCGTGCGGGCGCGGCTTTCCGGGTTCTGACACCAGCGGCAGCCCAGCGAACAGCCTTTAA  >  NZ_CP009273/858625‑858903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`