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	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%	60.5 / 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 (10/7); total (10/7)

ATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCA  >  NZ_CP009273/923484‑923755

aTGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGtgaactggac                                                                                                                                       <  1:94731/139‑1 (MQ=255)

aTGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGtgaactggac                                                                                                                                       <  1:152117/139‑1 (MQ=255)

aTGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGtgaactggac                                                                                                                                       <  1:75918/139‑1 (MQ=255)

        gTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGtgaactggac                                                                                                                                       >  2:198255/1‑131 (MQ=255)

        gTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGtgaactggac                                                                                                                                       <  1:198255/131‑1 (MQ=255)

                ttgtAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGc                                                                                                                       >  1:366275/1‑139 (MQ=255)

                          gtTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGTCGTTTACCTGAAGAGAACTCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTACCGTCAGCGAAACGCGAt                                                                                                             >  2:192622/1‑139 (MQ=255)

                          gtTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGt                                                                                                                                <  2:480045/120‑1 (MQ=255)

                          gtTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGt                                                                                                                                >  1:480045/1‑120 (MQ=255)

                          gtTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGAt                                                                                                             >  2:294960/1‑139 (MQ=255)

                             gATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCgg                                                                                                          >  1:431151/1‑139 (MQ=255)

                                     gCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGa                                                                                                  <  2:431151/139‑1 (MQ=255)

                                                                         ggCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGa                                                              >  1:321628/1‑139 (MQ=255)

                                                                                     aaGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGt                                                    <  1:418764/137‑1 (MQ=255)

                                                                                     aaGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGt                                                    >  2:192546/1‑137 (MQ=255)

                                                                                                   tAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACgg                                     <  2:366275/138‑1 (MQ=255)

                                                                                                    aaGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGc                                    <  2:321628/138‑1 (MQ=255)

                                                                                                     aGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCa                                   <  1:42936/138‑1 (MQ=255)

                                                                                                         ccTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAgg                               >  2:256277/1‑138 (MQ=255)

                                                                                                             ttGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAt                           >  1:85263/1‑138 (MQ=255)

                                                                                                                agaTTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACt                       <  1:192546/139‑1 (MQ=255)

                                                                                                                   ttGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGc                    >  2:181528/1‑139 (MQ=255)

                                                                                                                                     ctggacATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCa  >  1:286369/1‑139 (MQ=255)

ATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCA  >  NZ_CP009273/923484‑923755

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

GTTGCGGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCAC  >  NZ_CP009273/923472‑923756

GTTGCGGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGAC                                                                                                                                        <  SRR3722131.181699/151‑1 (MQ=60)

          ggctcggagatgtgtataagagacagGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAAC                                                                                                                              <  SRR3722131.85553/125‑1 (MQ=60)

           CATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACG                                                                                                                             <  SRR3722131.153888/151‑1 (MQ=60)

           CATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACG                                                                                                                             <  SRR3722131.200552/151‑1 (MQ=60)

           CATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACG                                                                                                                             <  SRR3722131.76763/151‑1 (MQ=60)

           CATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACG                                                                                                                             <  SRR3722131.95785/151‑1 (MQ=60)

                 CGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCG                                                                                                                       >  SRR3722131.370347/1‑151 (MQ=60)

                           GTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGActgtctctt                                                                                                             >  SRR3722131.485179/1‑142 (MQ=60)

                              GTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGC                                                                                                          >  SRR3722131.435806/1‑151 (MQ=60)

                                                                          ATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGAT                                                              >  SRR3722131.325272/1‑151 (MQ=60)

                                                                                                GAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGT                                          <  SRR3722131.423297/149‑1 (MQ=60)

                                                                                                            CTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaaataaaaatcaacaatatatt                            >  SRR3722131.201147/1‑54 (MQ=60)

                                                                                                              TTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATG                           >  SRR3722131.86194/1‑150 (MQ=60)

                                                                                                                AAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGAC                         <  SRR3722131.43381/150‑1 (MQ=60)

                                                                                                                           GAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATG             <  SRR3722131.194753/151‑1 (MQ=60)

                                                                                                                                      GGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCAC  >  SRR3722131.289678/1‑151 (MQ=60)

GTTGCGGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCAC  >  NZ_CP009273/923472‑923756

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`