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 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

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%	104.6 / NA	30	F85F (TTT→TTC)	BW25113_RS24960	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/11); total (19/11)

ACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAG  >  NZ_CP009273/524229‑524475

aCTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAatgatgat                                                                                                              >  2:193848/1‑139 (MQ=255)

            tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                   >  1:142737/1‑138 (MQ=255)

            tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                   >  2:255370/1‑138 (MQ=255)

            tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                   >  2:170737/1‑138 (MQ=255)

            tACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGtt                                                                                                   >  1:278751/1‑138 (MQ=255)

                 gAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTaa                                                                                                                         <  2:26138/111‑1 (MQ=255)

                 gAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTaa                                                                                                                         >  1:26138/1‑111 (MQ=255)

                         tgGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                     >  1:306353/1‑139 (MQ=255)

                                tttACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAg                                                                              >  1:316936/1‑139 (MQ=255)

                                        gCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAgg                                                                       >  2:352080/1‑138 (MQ=255)

                                        gCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAgg                                                                       >  1:19936/1‑138 (MQ=255)

                                                                 gCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCaaa                                             <  1:51971/139‑1 (MQ=255)

                                                                   ggTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGa                                           <  1:193848/139‑1 (MQ=255)

                                                                        atatatCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGAt                                      >  1:61798/1‑139 (MQ=255)

                                                                            atCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGa                                           <  2:214116/130‑1 (MQ=255)

                                                                            atCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGa                                           >  1:214116/1‑130 (MQ=255)

                                                                            atCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATc                                     >  1:260543/1‑136 (MQ=255)

                                                                            atCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATc                                     >  2:402746/1‑136 (MQ=255)

                                                                                   taCACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACaa                            <  2:278751/138‑1 (MQ=255)

                                                                                          aTGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                    <  2:19936/139‑1 (MQ=255)

                                                                                          aTGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtg                    >  2:59862/1‑139 (MQ=255)

                                                                                           tGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAgtgt                   >  2:213000/1‑139 (MQ=255)

                                                                                                   atgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTaaa           <  1:237060/139‑1 (MQ=255)

                                                                                                    tgatTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTaaa           >  1:207859/1‑138 (MQ=255)

                                                                                                      attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                     >  1:114085/1‑62 (MQ=255)

                                                                                                      attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                     <  2:114085/62‑1 (MQ=255)

                                                                                                      attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                     <  2:173882/62‑1 (MQ=255)

                                                                                                      attattTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGa                                                                                     >  1:173882/1‑62 (MQ=255)

                                                                                                          tttttttCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTa    <  1:402746/139‑1 (MQ=255)

                                                                                                             ttttCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAg  <  2:61798/138‑1 (MQ=255)

ACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAG  >  NZ_CP009273/524229‑524475

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

CTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGG  >  NZ_CP009273/524207‑524484

CTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCC                                                                                                                                     <  SRR3722119.335524/147‑1 (MQ=60)

                       CTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTT                                                                                                           >  SRR3722119.144211/1‑150 (MQ=60)

                       CTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTT                                                                                                           >  SRR3722119.281630/1‑150 (MQ=60)

                            TGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATctgtctcttatacacatc                                                                                                     >  SRR3722119.26370/1‑133 (MQ=60)

                                    CCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGAC                                                                                             >  SRR3722119.309482/1‑151 (MQ=60)

                                           ATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGG                                                                                      >  SRR3722119.320177/1‑151 (MQ=60)

                                                   GTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGG                                                                               >  SRR3722119.20124/1‑150 (MQ=60)

                                                                                   CGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATC                                              >  SRR3722119.62371/1‑151 (MQ=60)

                                                                                      AGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAG                                           <  SRR3722119.52432/151‑1 (MQ=60)

                                                                                       GCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCC                                             >  SRR3722119.263239/1‑148 (MQ=60)

                                                                                       GCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCC                                             >  SRR3722119.216413/1‑148 (MQ=60)

                                                                                        CGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGAT                                         <  SRR3722119.195919/151‑1 (MQ=60)

                                                                                                               AATGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAAT                   >  SRR3722119.210090/1‑150 (MQ=60)

                                                                                                                 TGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCtctgtctcttatacacatctccgagcccacgagactaaggcgaatatcgtatgccgccttctgcttg                 >  SRR3722119.175666/1‑83 (MQ=60)

                                                                                                                 TGTAGAAGATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttg                 >  SRR3722119.115203/1‑84 (MQ=60)

                                                                                                                        GATGATTATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGAT         <  SRR3722119.239542/151‑1 (MQ=60)

                                                                                                                               ATTTTTTTCTTATTTTCCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGG  <  SRR3722119.406767/151‑1 (MQ=60)

CTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTTCTTATTTTTCCCTAACAAATGATGATGGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGG  >  NZ_CP009273/524207‑524484

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`