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 I102 R1	278	39.1	2251254	95.8%	2156701	87.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	527,133	A→G	V182A (GTT→GCT)	allS ←	HTH‑type transcriptional activator AllS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	527,133	0	A	G	100.0%	111.4 / NA	32	V182A (GTT→GCT)	allS	HTH‑type transcriptional activator AllS
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/19); total (13/19)

GGCGACGCGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAACGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGC  >  NZ_CP009273/527045‑527216

ggCGACGCGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTAACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCg                                                                                   >  2:908566/1‑91 (MQ=255)

 gCGACGCGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGt                                                                                  <  2:164294/91‑1 (MQ=255)

         tttGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGc                                                                          <  2:1002823/91‑1 (MQ=255)

           tGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCgg                                                                        <  2:207330/91‑1 (MQ=255)

             gTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGgat                                                                      <  1:601361/91‑1 (MQ=255)

                 aGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATc                                                                  >  1:197824/1‑91 (MQ=255)

                        ggCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCgccgcc                                                           <  2:600307/91‑1 (MQ=255)

                               tCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACaa                                                    <  1:383291/91‑1 (MQ=255)

                                  tCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAgc                                                 <  1:1060020/91‑1 (MQ=255)

                                  tCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAgc                                                 <  2:240249/91‑1 (MQ=255)

                                  tCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAgc                                                 <  1:801009/91‑1 (MQ=255)

                                  tCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAgc                                                 <  1:399882/91‑1 (MQ=255)

                                        ttGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCAtt                                           >  1:511225/1‑91 (MQ=255)

                                        ttGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCAtt                                           >  2:1108747/1‑91 (MQ=255)

                                          gACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGc                                         >  1:1096273/1‑91 (MQ=255)

                                          gACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGc                                         >  1:668173/1‑91 (MQ=255)

                                          gACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGc                                         >  1:877500/1‑91 (MQ=255)

                                             cgccgGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCAcc                                      <  1:245694/91‑1 (MQ=255)

                                               ccgGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGa                                    >  1:511969/1‑91 (MQ=255)

                                               ccgGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGa                                    >  1:346023/1‑91 (MQ=255)

                                                      gcgcCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCTAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAg                             <  1:1052393/91‑1 (MQ=255)

                                                            caccTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCa                       <  2:1029346/88‑1 (MQ=255)

                                                            cAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCa                       <  1:252136/91‑1 (MQ=255)

                                                            cAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCa                       <  2:197824/91‑1 (MQ=255)

                                                              aCTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAg                     <  1:369520/91‑1 (MQ=255)

                                                                    cTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTaaa               <  2:581801/91‑1 (MQ=255)

                                                                              cGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCAcc                                      >  1:876079/1‑58 (MQ=255)

                                                                              cGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCAcc                                      <  2:876079/58‑1 (MQ=255)

                                                                                gCTCTTCAGCGTTCGCGAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACTGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAg   >  1:1085065/1‑91 (MQ=255)

                                                                                gCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGATAAAGCGCCATTGCAcc                                      <  2:117320/56‑1 (MQ=255)

                                                                                gCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGATAAAGCGCCATTGCAcc                                      >  1:117320/1‑56 (MQ=255)

                                                                                gCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAg   >  2:828893/1‑91 (MQ=255)

                                                                                 ctctTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAgc  <  1:449406/91‑1 (MQ=255)

GGCGACGCGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAACGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGC  >  NZ_CP009273/527045‑527216

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 29 ≤` `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

CGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAACGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGCGCCTCAGTTCCC  >  NZ_CP009273/527052‑527228

CGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATC                                                                              >  SRR3722125.201722/1‑101 (MQ=60)

      GTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGC                                                                        <  SRR3722125.614306/101‑1 (MQ=60)

                       GTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATT                                                       >  SRR3722125.522074/1‑101 (MQ=60)

                        TCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTG                                                      <  SRR3722125.391330/101‑1 (MQ=60)

                         CTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGC                                                     >  SRR3722125.896909/1‑101 (MQ=60)

                         CTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGC                                                     >  SRR3722125.1120966/1‑101 (MQ=60)

                         CTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGC                                                     >  SRR3722125.682553/1‑101 (MQ=60)

                           TCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCAC                                                   <  SRR3722125.1083878/101‑1 (MQ=60)

                           TCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCAC                                                   <  SRR3722125.818505/101‑1 (MQ=60)

                           TCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCAC                                                   <  SRR3722125.408284/101‑1 (MQ=60)

                              ATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGA                                                >  SRR3722125.353210/1‑101 (MQ=60)

                              ATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGA                                                >  SRR3722125.522841/1‑101 (MQ=60)

                                      CGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGG                                        <  SRR3722125.250626/101‑1 (MQ=60)

                                               GCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCTAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGAC                               <  SRR3722125.1076030/101‑1 (MQ=60)

                                                     CAACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGG                         <  SRR3722125.257212/101‑1 (MQ=60)

                                                       ACTGCGCTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTA                       <  SRR3722125.377263/101‑1 (MQ=60)

                                                             CTTCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGctgtctcttatacacatctccga                 >  SRR3722125.895459/1‑78 (MQ=60)

                                                               TCTGTTAGCGGCTCTTCAGCGTTCGCGAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACTGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAG               >  SRR3722125.1109490/1‑101 (MQ=60)

                                                               TCTGTTAGCGGCTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGATAAAGCGCCATTGCACCGATCCTAAGGctgtctcttatacacatctccgagc               >  SRR3722125.119522/1‑76 (MQ=60)

                                                                          CTCTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGCGCCTCAGTTC    <  SRR3722125.458886/101‑1 (MQ=60)

                                                                            CTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGCGCCTCAGTTCCC  >  SRR3722125.318016/1‑101 (MQ=60)

                                                                            CTTCAGCGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGCGCCTCAGTTCCC  >  SRR3722125.116059/1‑101 (MQ=60)

CGTTTGGTTAAGGTGCGGGCGCTGTCTTCAATATTGACCGCCGGAAAGCGCCGCAACTGCGCTTCTGTTAGCGGCTCTTCAACGTTCGCCAGCGGATGATCCGCCGCCATGACAAAGCGCCATTGCACCGATCCTAAGGGATCAAGACTAAAGGTATTTGCCAGCGCCTCAGTTCCC  >  NZ_CP009273/527052‑527228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 7 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`