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 I179 R1	182	40.3	1547118	96.8%	1497610	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	923,620	A→G	V344V (GTT→GTC)	cydC ←	cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	923,620	0	A	G	100.0%	61.6 / NA	17	V344V (GTT→GTC)	cydC	cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/8); total (9/8)

ATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATG  >  NZ_CP009273/923484‑923753

aTGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGATAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGtgaactggac                                                                                                                                     <  1:619645/139‑1 (MQ=255)

           aGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACg                                                                                                                          <  2:649096/139‑1 (MQ=255)

                  gtAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCg                                                                                                                    >  1:613139/1‑138 (MQ=255)

                                                 cccGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACg                                                                                                                          >  1:767716/1‑101 (MQ=255)

                                                 cccGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACg                                                                                                                          <  2:767716/101‑1 (MQ=255)

                                                 cccGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAaca                                                                                                   >  1:65316/1‑124 (MQ=255)

                                                 cccGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAaca                                                                                                   <  2:65316/124‑1 (MQ=255)

                                                  ccGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAg                                                                                   >  2:38886/1‑139 (MQ=255)

                                                          cGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGt                                                                            >  2:329393/1‑138 (MQ=255)

                                                            cTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGAc                                                                         >  1:264644/1‑139 (MQ=255)

                                                                 tGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTcc                                                                     <  2:376613/138‑1 (MQ=255)

                                                                               tACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGt                                                       <  1:743343/138‑1 (MQ=255)

                                                                                        agaAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCagag                                             <  1:329393/139‑1 (MQ=255)

                                                                                        agaAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCagag                                             <  2:244529/139‑1 (MQ=255)

                                                                                            aTCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGAtac                                         >  1:104074/1‑139 (MQ=255)

                                                                                                    aaGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGc                                  <  1:266766/138‑1 (MQ=255)

                                                                                                                       tCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGccc                >  2:435293/1‑137 (MQ=255)

                                                                                                                                gTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGa      >  1:13282/1‑138 (MQ=255)

                                                                                                                                   aactggacATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATg  <  2:104074/139‑1 (MQ=255)

                                                                                                                                     ctgaacATCCCGTAACGTCAGCGAAACGCGATCgg                                                                                                        <  1:60608/35‑1 (MQ=255)

                                                                                                                                     ctgaacATCCCGTAACGTCAGCGAAACGCGATCgg                                                                                                        >  2:60608/1‑35 (MQ=255)

ATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATG  >  NZ_CP009273/923484‑923753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 35 ≤` `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

GGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGG  >  NZ_CP009273/923477‑923766

GGGTCCCATGCGCGGGTGAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCC                                                                                                                                             <  SRR3722133.162160/151‑1 (MQ=60)

     CCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAAC                                                                                                                                        <  SRR3722133.444986/151‑1 (MQ=60)

      CATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGATAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACG                                                                                                                                       <  SRR3722133.627789/151‑1 (MQ=60)

              GGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGA                                                                                                                                >  SRR3722133.621225/1‑150 (MQ=60)

                                   gagtagtatgtttgttatttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTT                                                                                                          <  SRR3722133.61400/57‑1 (MQ=60)

                                             CATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCtgtctcttatacacatctccgagccc                                                                                                 >  SRR3722133.777636/1‑124 (MQ=60)

                                             CATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTctgtc                                                                                                >  SRR3722133.66149/1‑146 (MQ=60)

                                                        CCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACC                                                                                     >  SRR3722133.268246/1‑151 (MQ=60)

                                                                                     TTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGA                                                         <  SRR3722133.752951/150‑1 (MQ=60)

                                                                                        CCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACG                                                     >  SRR3722133.105432/1‑151 (MQ=60)

                                                                                              GAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGC                                               <  SRR3722133.334029/151‑1 (MQ=60)

                                                                                                     CCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaagatcactcgagcgc                                          >  SRR3722133.64989/1‑55 (MQ=60)

                                                                                                          TAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGA                                    <  SRR3722133.270395/150‑1 (MQ=60)

                                                                                                                            GCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAA                  >  SRR3722133.13433/1‑150 (MQ=60)

                                                                                                                                           ACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGG  >  SRR3722133.87396/1‑151 (MQ=60)

GGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGG  >  NZ_CP009273/923477‑923766

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`