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	524,350	T→C	F85F (TTT→TTC)	BW25113_RS24960 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	524,350	0	T	C	100.0%	100.1 / NA	29	F85F (TTT→TTC)	BW25113_RS24960	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/16); total (13/16)

ACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTA  >  NZ_CP009273/524218‑524473

aCATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTaa                                                                                                                       >  2:852524/1‑139 (MQ=255)

      cATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAatg                                                                                                                 <  1:401893/139‑1 (MQ=255)

                       tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                 >  1:241134/1‑138 (MQ=255)

                            gAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGa                                                                                            >  1:628698/1‑138 (MQ=255)

                             aaaaTGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGa                                                                                            >  2:115237/1‑138 (MQ=255)

                             aaaaTGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGaa                                                                                           >  1:315466/1‑138 (MQ=255)

                                    tgGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                   <  1:708070/139‑1 (MQ=255)

                                      gAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACa                                                                                 <  1:250607/139‑1 (MQ=255)

                                         tttttACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTg                                                                              <  1:138090/139‑1 (MQ=255)

                                         tttttACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTg                                                                              <  1:592941/139‑1 (MQ=255)

                                               cATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGcc                                                                        <  2:315466/139‑1 (MQ=255)

                                                                                       atC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAg                                                                                             <  1:110976/78‑1 (MQ=255)

                                                                                       atC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAg                                                                                             >  2:110976/1‑78 (MQ=255)

                                                                                       atC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGAtt                                   >  1:673886/1‑135 (MQ=255)

                                                                                       atC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATc                                   >  2:14545/1‑136 (MQ=255)

                                                                                               taCACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGt                                                                               >  2:325058/1‑85 (MQ=255)

                                                                                               taCACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGt                                                                               <  1:325058/85‑1 (MQ=255)

                                                                                                      aTGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                  <  1:14545/139‑1 (MQ=255)

                                                                                                       tGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                  <  2:26733/138‑1 (MQ=255)

                                                                                                       tGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGCAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                  >  1:26733/1‑138 (MQ=255)

                                                                                                         tAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTgtgg               >  2:348635/1‑139 (MQ=255)

                                                                                                             agaTGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTa           <  1:802290/139‑1 (MQ=255)

                                                                                                              gctgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGt                                                                                                      >  1:335815/3‑47 (MQ=255)

                                                                                                              gatgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGt                                                                                                      <  2:335815/47‑1 (MQ=255)

                                                                                                              gatgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTa           >  1:334195/1‑138 (MQ=255)

                                                                                                                  attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAatat      <  1:852524/139‑1 (MQ=255)

                                                                                                                  attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAatat      <  2:334195/139‑1 (MQ=255)

                                                                                                                  attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAata       <  2:458485/138‑1 (MQ=255)

                                                                                                                      tttttttCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTa  <  2:628698/139‑1 (MQ=255)

ACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATC‑AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTA  >  NZ_CP009273/524218‑524473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `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

ACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC  >  NZ_CP009273/524223‑524480

ACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGT                                                                                                             <  SRR3722120.407845/151‑1 (MQ=60)

       CTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTT                                                                                                       >  SRR3722120.244573/1‑150 (MQ=60)

            TGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAA                                                                                                  >  SRR3722120.637406/1‑150 (MQ=60)

             GGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAA                                                                                                 >  SRR3722120.320027/1‑150 (MQ=60)

                    atacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGAC                                                                                         <  SRR3722120.112443/100‑1 (MQ=60)

                              ATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCC                                                                               <  SRR3722120.717735/151‑1 (MQ=60)

                                GGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAG                                                                             <  SRR3722120.254248/151‑1 (MQ=60)

                                  attcgccttagtctcgtgggctcggagatgtgtataagagacaGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGG                                                                           <  SRR3722120.329735/108‑1 (MQ=60)

                                   GTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGA                                                                          <  SRR3722120.139954/151‑1 (MQ=60)

                                   GTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGA                                                                          <  SRR3722120.601216/151‑1 (MQ=60)

                                                                       GCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATTC                                         >  SRR3722120.683116/1‑148 (MQ=60)

                                                                                      ATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGCAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTG                       >  SRR3722120.27037/1‑151 (MQ=60)

                                                                                             CAAATGTAGAAGCTGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAActgtctcttatacacatctccgagcccacgagactaaggcgaatctcggatgccgtcttctgcttgaaaaaaaaaaaaaggg                >  SRR3722120.340618/1‑69 (MQ=60)

                                                                                             CAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAA                 >  SRR3722120.338978/1‑150 (MQ=60)

                                                                                               AATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATA              <  SRR3722120.14715/151‑1 (MQ=60)

                                                                                                      AAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAG       <  SRR3722120.813091/151‑1 (MQ=60)

                                                                                                           GATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC  <  SRR3722120.863947/151‑1 (MQ=60)

ACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC  >  NZ_CP009273/524223‑524480

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`