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 I177 R1	141	27.5	996908	97.7%	973979	124.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,060,660	T→C	L390P (CTC→CCC)	yccE →	YccE family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,060,660	0	T	C	100.0%	31.5 / NA	10	L390P (CTC→CCC)	yccE	YccE family protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/5); total (5/5)

GTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACT  >  NZ_CP009273/1060551‑1060792

gTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTAc                                                                                                          <  2:342701/138‑1 (MQ=255)

       gTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTaaa                                                                                                  <  2:162978/139‑1 (MQ=255)

           tgtgGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAAt                                                                                              <  2:236008/139‑1 (MQ=255)

               gCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCtt                                                                                                            >  1:464151/1‑121 (MQ=255)

               gCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCtt                                                                                                            <  2:464151/121‑1 (MQ=255)

                     aTCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAaatg                                                                                     >  1:224310/1‑138 (MQ=255)

                                                                    tGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAgg                                     >  2:235193/1‑139 (MQ=255)

                                                                          tttAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATg                               >  2:183184/1‑139 (MQ=255)

                                                                               tGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTaaa                          <  1:235193/139‑1 (MQ=255)

                                                                                                       tttACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACt  >  2:199864/1‑139 (MQ=255)

GTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACT  >  NZ_CP009273/1060551‑1060792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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

ATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTTTTTATTGG  >  NZ_CP009273/1060555‑1060802

ATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACctgtctct                                                                                                   >  SRR3722131.469136/1‑143 (MQ=60)

      ATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGA                                                                                              >  SRR3722131.226957/1‑150 (MQ=60)

                 ATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtat                                                                                  >  SRR3722131.437788/1‑100 (MQ=60)

                                                                          ATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTA                         <  SRR3722131.237977/151‑1 (MQ=60)

                                                                                                  GTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaa  >  SRR3722131.7579/1‑82 (MQ=60)

ATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTTTTTATTGG  >  NZ_CP009273/1060555‑1060802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`