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 I181 R1	159	32.7	1279082	96.9%	1239430	121.0

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%	121.0 / NA	28	coding (257/591 nt)	ycaK	NAD(P)H oxidoreductase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (11/17); total (11/17)

CGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGG  >  NZ_CP009273/945256‑945508

cGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCTAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggtg                                                                                                                   >  1:420650/1‑139 (MQ=255)

cGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggtg                                                                                                                   >  2:24756/1‑139 (MQ=255)

cGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggtg                                                                                                                   >  2:171856/1‑139 (MQ=255)

    aTTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTa                                                                                                                <  1:377865/138‑1 (MQ=255)

          aCCCAGTGATGACGCCGGAAGATGAACCGGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTc                                                                                                         >  2:568972/1‑139 (MQ=255)

          aCCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTc                                                                                                         >  2:41203/1‑139 (MQ=255)

               gTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc                                                                                                    <  2:45151/139‑1 (MQ=255)

                       gCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTaa                                                                                            <  1:157839/139‑1 (MQ=255)

                          ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAg                                                                                         >  1:340266/1‑139 (MQ=255)

                          ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAg                                                                                         <  2:340266/139‑1 (MQ=255)

                          ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAg                                                                                         <  1:171856/139‑1 (MQ=255)

                                      ggACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:568972/138‑1 (MQ=255)

                                      aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:480205/139‑1 (MQ=255)

                                      aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:538194/139‑1 (MQ=255)

                                      aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:557908/139‑1 (MQ=255)

                                      aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:329115/139‑1 (MQ=255)

                                      aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:24756/139‑1 (MQ=255)

                                        aCTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCaa                                                                                                  >  2:65546/1‑116 (MQ=255)

                                        aCTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCaa                                                                                                  <  1:65546/116‑1 (MQ=255)

                                                  tatGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaat                                                                  >  2:598080/1‑138 (MQ=255)

                                                       aTAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg                                                            <  2:192366/139‑1 (MQ=255)

                                                                              catcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             <  1:638506/99‑1 (MQ=255)

                                                                              catcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa                                                                             >  2:638506/1‑99 (MQ=255)

                                                                                              agCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATa                       >  1:539736/1‑137 (MQ=255)

                                                                                                   ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCg                >  1:147584/1‑139 (MQ=255)

                                                                                                             acacGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg      <  2:420650/139‑1 (MQ=255)

                                                                                                             acacGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg      <  2:539736/139‑1 (MQ=255)

                                                                                                                 gTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTgg  <  1:598080/139‑1 (MQ=255)

CGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGG  >  NZ_CP009273/945256‑945508

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

ATTTATATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGAC  >  NZ_CP009273/945245‑945519

ATTTATATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCTAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGG                                                                                                                             >  SRR3722135.426416/1‑151 (MQ=60)

              AATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGG                                                                                                                <  SRR3722135.383146/150‑1 (MQ=60)

                          GTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGG                                                                                                   >  SRR3722135.345102/1‑151 (MQ=60)

                           gtataagagacagAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGA                                                                                                  <  SRR3722135.66425/138‑1 (MQ=60)

                                 CGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATT                                                                                            <  SRR3722135.160019/151‑1 (MQ=60)

                                    CGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAC                                                                                         <  SRR3722135.174241/151‑1 (MQ=60)

                                                cgtgggctcggagatgtgtataagagacagCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.646796/121‑1 (MQ=60)

                                                CGGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.576463/151‑1 (MQ=60)

                                                CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.333805/151‑1 (MQ=60)

                                                CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.25077/151‑1 (MQ=60)

                                                CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.486656/151‑1 (MQ=60)

                                                CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.545316/151‑1 (MQ=60)

                                                CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT                                                                             <  SRR3722135.565281/151‑1 (MQ=60)

                                                                                              GCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAA                                 >  SRR3722135.546879/1‑149 (MQ=60)

                                                                                                   ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGT                          >  SRR3722135.149646/1‑151 (MQ=60)

                                                                                                                        ACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccg     >  SRR3722135.270768/1‑96 (MQ=60)

                                                                                                                           CGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGAC  <  SRR3722135.605935/151‑1 (MQ=60)

ATTTATATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGAC  >  NZ_CP009273/945245‑945519

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: `‑`