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	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%	96.9 / NA	28	F85F (TTT→TTC)	BW25113_RS24960	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/13); total (15/13)

TAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC  >  NZ_CP009273/524215‑524480

taaACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTcccc                                                                                                                                 >  2:128839/1‑139 (MQ=255)

      ttACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACa                                                                                                                            >  2:73713/1‑138 (MQ=255)

        aCATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTccc                                                                                                                                  >  2:378323/1‑130 (MQ=255)

        aCATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTccc                                                                                                                                  <  1:378323/130‑1 (MQ=255)

         cATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAatg                                                                                                                        <  2:491136/139‑1 (MQ=255)

              aCTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAatgatgat                                                                                                                   <  2:170545/139‑1 (MQ=255)

                        aaTACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGt                                                                                                         >  1:544651/1‑139 (MQ=255)

                          tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                        >  1:198724/1‑138 (MQ=255)

                          tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                        >  2:161268/1‑138 (MQ=255)

                            ccAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGttt                                                                                                       >  2:548258/1‑137 (MQ=255)

                               gAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGaa                                                                                                  <  1:51213/139‑1 (MQ=255)

                                       tgGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                          <  1:161268/139‑1 (MQ=255)

                                              tttACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGa                                                                                    <  2:198724/138‑1 (MQ=255)

                                                    tGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAg                                                                             >  2:116500/1‑139 (MQ=255)

                                                      gCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAgg                                                                            >  2:159835/1‑138 (MQ=255)

                                                                                     gATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCt                                                                                                                                >  2:322559/1‑55 (MQ=255)

                                                                                     gATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCt                                                                                                                                <  1:322559/55‑1 (MQ=255)

                                                                                               tataCACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATAc                                   >  1:382383/1‑138 (MQ=255)

                                                                                               tataCACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTACCAGTGAGGGCCAGGAACCAAGGGGGGAAAATGGAATCAAAGATTGATCCGGATAc                                   >  1:135565/1‑138 (MQ=255)

                                                                                                       aaTGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgt                          >  1:557109/1‑139 (MQ=255)

                                                                                                        aaggagaagaagaATTATTTTTTCTTTATTTCCCCCAACAAAAGGAGAAGGGGGGTAGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                         <  2:135565/135‑1 (MQ=255)

                                                                                                        aTGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                         >  1:299419/1‑139 (MQ=255)

                                                                                                         tGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTGAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCg                                                         <  2:361252/106‑1 (MQ=255)

                                                                                                         tGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTGAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCg                                                         >  1:361252/1‑106 (MQ=255)

                                                                                                         tGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtgt                        >  2:490702/1‑139 (MQ=255)

                                                                                                             gaagaTGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTgtggt                     <  2:148065/138‑1 (MQ=255)

                                                                                                                  tgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGc                                                                                >  2:279790/1‑74 (MQ=255)

                                                                                                                  tgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGc                                                                                <  1:279790/74‑1 (MQ=255)

                                                                                                                    attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAatat             <  1:490702/139‑1 (MQ=255)

                                                                                                                    attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAatat             <  1:116500/139‑1 (MQ=255)

                                                                                                                                  aTTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATAcc  <  2:557109/136‑1 (MQ=255)

TAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC  >  NZ_CP009273/524215‑524480

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

AGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGGATGGTG  >  NZ_CP009273/524213‑524497

AGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGA                                                                                                                                        <  SRR3722139.382845/151‑1 (MQ=60)

   tttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATG                                                                                                                                      <  SRR3722139.326537/77‑1 (MQ=60)

               AACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTT                                                                                                                         >  SRR3722139.550920/1‑151 (MQ=60)

                 CTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTT                                                                                                                        >  SRR3722139.201175/1‑150 (MQ=60)

                                AGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAG                                                                                                        <  SRR3722139.51799/151‑1 (MQ=60)

                                        ATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCC                                                                                                <  SRR3722139.163248/151‑1 (MQ=60)

                                                  cggcatacgatatctagtacggtctcgtgggctcggagatgtgtataagagacagAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAG                                                                                      <  SRR3722139.283314/96‑1 (MQ=60)

                                                                                      GGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACA                                                   >  SRR3722139.386944/1‑150 (MQ=60)

                                                                                      GGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTACCAGTGAGGGCCAGGAACCAAGGGGGGAAAATGGAATCAAAGATTGATCCGGATACA                                                   >  SRR3722139.137204/1‑150 (MQ=60)

                                                                                              CAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTG                                          >  SRR3722139.563492/1‑151 (MQ=60)

                                                                                               AATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGT                                         >  SRR3722139.303154/1‑151 (MQ=60)

                                                                                                ATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTGAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATctgtctcttatacacatctccg                                         >  SRR3722139.365599/1‑128 (MQ=60)

                                                                                                                     GATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC                   <  SRR3722139.117909/151‑1 (MQ=60)

                                                                                                                     GATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACC                   <  SRR3722139.496394/151‑1 (MQ=60)

                                                                                                                                       TTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGGATGGTG  <  SRR3722139.74565/150‑1 (MQ=60)

AGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGGATGGTG  >  NZ_CP009273/524213‑524497

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`