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
A1 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	587,628	A→G	F336S (TTC→TCC)	nrfB ←	cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	587,628	0	A	G	100.0%	113.6 / NA	30	F336S (TTC→TCC)	nrfB	cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/15); total (15/15)

ACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTTC  >  NZ_CP009273/587517‑587755

aCCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGAtt                                                                                                      <  1:405344/139‑1 (MQ=255)

aCCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGAt                                                                                                       <  2:514296/138‑1 (MQ=255)

       tCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTc                                                                                                >  1:316197/1‑138 (MQ=255)

        cgcgAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCg                                                                                               >  1:287856/1‑138 (MQ=255)

            aGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCg                                                                                          <  2:293604/139‑1 (MQ=255)

                              cTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCg                                                                         <  1:570298/138‑1 (MQ=255)

                                           tGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTcgcg                                                           >  2:475129/1‑139 (MQ=255)

                                            gCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTcgcg                                                           <  2:287856/138‑1 (MQ=255)

                                               gTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacg                                                       <  1:321978/139‑1 (MQ=255)

                                               gTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacg                                                       <  2:316197/139‑1 (MQ=255)

                                               gTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacg                                                       <  1:540585/139‑1 (MQ=255)

                                                  gcgcCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAg                                                                                                             >  2:545265/1‑82 (MQ=255)

                                                  gcgcCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAg                                                                                                             <  1:545265/82‑1 (MQ=255)

                                                   cgcCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacg                                                       >  2:128933/1‑135 (MQ=255)

                                                    gcCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGAt                                                  <  2:594679/139‑1 (MQ=255)

                                                    gcCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGAt                                                  <  2:130887/139‑1 (MQ=255)

                                                     ccAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGAt                                                  >  2:104824/1‑138 (MQ=255)

                                                                  ttCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTcc                                    >  1:297165/1‑139 (MQ=255)

                                                                     aGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCcgcg                                 >  1:348935/1‑139 (MQ=255)

                                                                            ggCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCg                                                                                                           <  2:381901/58‑1 (MQ=255)

                                                                            ggCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCg                                                                                                           >  1:381901/1‑58 (MQ=255)

                                                                                 gAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGAt                                                  >  1:244450/1‑110 (MQ=255)

                                                                                 gAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGAt                                                  <  2:244450/110‑1 (MQ=255)

                                                                                 gAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTaaa                      >  2:737691/1‑138 (MQ=255)

                                                                                                 ttttAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTcgcg     <  1:488487/139‑1 (MQ=255)

                                                                                                  tttAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGt    >  1:359484/1‑139 (MQ=255)

                                                                                                   ttAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGtt   >  2:377195/1‑139 (MQ=255)

                                                                                                    tAAAGCCTTGGGAAACAATGCAGCTGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAACTTTACGCTGCTCGCGTTc  >  1:68757/1‑139 (MQ=255)

                                                                                                           ttGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTcg       <  1:727544/127‑1 (MQ=255)

                                                                                                           ttGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTcg       >  2:727544/1‑127 (MQ=255)

ACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTTC  >  NZ_CP009273/587517‑587755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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

CTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTTCTTTGGCTT  >  NZ_CP009273/587481‑587763

CTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAA                                                                                                                                       >  SRR3722120.297808/1‑150 (MQ=60)

    CATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAA                                                                                                                                   <  SRR3722120.200894/150‑1 (MQ=60)

                            gagattcgccttagtctcgtgggctcggagatgtgtataagagacagCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTG                                                                                                          <  SRR3722120.552944/104‑1 (MQ=60)

                                CATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCG                                                                                                       >  SRR3722120.320771/1‑150 (MQ=60)

                                 ATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGA                                                                                                      >  SRR3722120.291990/1‑150 (MQ=60)

                                   CACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACC                                                                                                   <  SRR3722120.411331/151‑1 (MQ=60)

                                                                 ACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTC                                                                      <  SRR3722120.578255/150‑1 (MQ=60)

                                                                                  GGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTT                                                    <  SRR3722120.326618/151‑1 (MQ=60)

                                                                                  GGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTT                                                    <  SRR3722120.548215/151‑1 (MQ=60)

                                                                                           AGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCG                                           >  SRR3722120.301414/1‑151 (MQ=60)

                                                                                              GAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGC                                        >  SRR3722120.353982/1‑151 (MQ=60)

                                                                                                     GTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaa                                  >  SRR3722120.387519/1‑80 (MQ=60)

                                                                                                          GCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGctgtctcttatacacatct                            >  SRR3722120.247950/1‑132 (MQ=60)

                                                                                                                           CATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTT           >  SRR3722120.364702/1‑151 (MQ=60)

                                                                                                                             TTTATGGGTTTTAAAGCCTTGGGAAACAATGCAGCTGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAACTTTACGCTGCTCGCGTTCT         >  SRR3722120.69663/1‑151 (MQ=60)

                                                                                                                                  AGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTTCTTTGGC    <  SRR3722120.737412/151‑1 (MQ=60)

                                                                                                                                    GTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTTCTTTGGCTT  <  SRR3722120.495506/151‑1 (MQ=60)

CTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATGTCCGCGCGTGCTGTAAAAATTTACGCTGCTCGCGTTCTTTGGCTT  >  NZ_CP009273/587481‑587763

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`