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	945,384	(T)_5→4	coding (261/591 nt)	ycaK →	NAD(P)H oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	945,380	0	T	.	100.0%	136.4 / NA	31	coding (257/591 nt)	ycaK	NAD(P)H oxidoreductase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (16/15); total (16/15)

ACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCG  >  NZ_CP009273/945266‑945504

aCCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTc                                                                                                     >  2:249477/1‑139 (MQ=255)

     gTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCgg                                                                                                 >  2:120089/1‑138 (MQ=255)

     gTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCgg                                                                                                 >  1:336685/1‑138 (MQ=255)

     gTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc                                                                                                <  1:249477/139‑1 (MQ=255)

                            aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         <  2:564319/139‑1 (MQ=255)

                            aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         <  1:57692/139‑1 (MQ=255)

                            aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         <  1:263855/139‑1 (MQ=255)

                            aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         <  1:380651/139‑1 (MQ=255)

                              aCTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACaga                                                                       <  1:517165/139‑1 (MQ=255)

                                        tatGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaat                                                              >  1:75606/1‑138 (MQ=255)

                                            gATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATgg                                                         >  1:154279/1‑139 (MQ=255)

                                             aTAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg                                                        <  1:525199/139‑1 (MQ=255)

                                                aaCGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggctg                                                     >  2:136757/1‑139 (MQ=255)

                                                  cGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggctggc                                                   <  1:340481/139‑1 (MQ=255)

                                                       ttCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAACAATGGGCTGGCTTATg                                              >  1:480751/1‑139 (MQ=255)

                                                            cAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGgag                                           <  1:114315/137‑1 (MQ=255)

                                                                         gCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTAc                            >  1:188506/1‑139 (MQ=255)

                                                                                    agCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         <  1:226040/83‑1 (MQ=255)

                                                                                    agCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         >  2:226040/1‑83 (MQ=255)

                                                                                    agCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATa                   >  1:40903/1‑137 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAc                                                                          <  2:151576/77‑1 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAc                                                                          >  1:151576/1‑77 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         >  1:255139/1‑78 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                         <  2:255139/78‑1 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTa                                                                    >  2:188366/1‑83 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTa                                                                    <  1:188366/83‑1 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCg            >  1:399651/1‑139 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCg            >  1:200812/1‑139 (MQ=255)

                                                                                         ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCg            >  2:458083/1‑139 (MQ=255)

                                                                                                   acacGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg  <  2:188506/139‑1 (MQ=255)

                                                                                                   acacGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg  <  2:412029/139‑1 (MQ=255)

ACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCG  >  NZ_CP009273/945266‑945504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 36 ≤` `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

ATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATT  >  NZ_CP009273/945260‑945530

ATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGC                                                                                                                          >  SRR3722139.340793/1‑150 (MQ=60)

          AGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAG                                                                                                               <  SRR3722139.252636/151‑1 (MQ=60)

                                 agatctagtacggtctcgtgggctcggagatgtgtataagagacagGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                                        <  SRR3722139.228808/105‑1 (MQ=60)

                                 CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                                        <  SRR3722139.58346/151‑1 (MQ=60)

                                 CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                                        <  SRR3722139.267169/151‑1 (MQ=60)

                                 CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                                        <  SRR3722139.385197/151‑1 (MQ=60)

                                   GACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAA                                                                                      <  SRR3722139.523107/151‑1 (MQ=60)

                                   GACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATA                                                                                       >  SRR3722139.76481/1‑150 (MQ=60)

                                      agatctagtacggtctcgtgggctcggagatgtgtataagagacagATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGG                                                                                   <  SRR3722139.190707/105‑1 (MQ=60)

                                       GGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGG                                                                                  >  SRR3722139.156162/1‑151 (MQ=60)

                                                  GATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGG                                                                       <  SRR3722139.531251/151‑1 (MQ=60)

                                                  GATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAACAATGGGCTGGCTTATGG                                                                       >  SRR3722139.486354/1‑151 (MQ=60)

                                                       ACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATG                                                                  <  SRR3722139.344621/151‑1 (MQ=60)

                                                                 CCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAA                                                          <  SRR3722139.115693/149‑1 (MQ=60)

                                                                    GAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACC                                                     >  SRR3722139.190848/1‑151 (MQ=60)

                                                                               GCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAA                                            >  SRR3722139.41355/1‑149 (MQ=60)

                                                                                    ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAActgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatg                                     >  SRR3722139.153426/1‑99 (MQ=60)

                                                                                    ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtat                                     >  SRR3722139.258348/1‑100 (MQ=60)

                                                                                    ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGT                                     >  SRR3722139.404388/1‑151 (MQ=60)

                                                                                    ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGT                                     >  SRR3722139.203284/1‑151 (MQ=60)

                                                                                                                        GTTTTCCTTTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATT  <  SRR3722139.58199/151‑1 (MQ=60)

                                                                                                                        GTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATT  >  SRR3722139.490609/1‑151 (MQ=60)

ATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATT  >  NZ_CP009273/945260‑945530

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`