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	736,034	A→T	I358F (ATC→TTC)	phrB →	deoxyribodipyrimidine photo‑lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	736,034	0	A	T	100.0%	136.3 / NA	34	I358F (ATC→TTC)	phrB	deoxyribodipyrimidine photo‑lyase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (19/15); total (19/15)

ACAGGCCTGGCAGGAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGATCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCGA  >  NZ_CP009273/735904‑736169

aCAGGCCTGGCAGGAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGACAGATTTATTGTTCGAc                                                                                                                                    >  1:521359/1‑136 (MQ=255)

aCAGGCCTGGCAGGAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGAc                                                                                                                                    <  2:521359/136‑1 (MQ=255)

            ggAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGgcgag                                                                                                                     <  2:222733/139‑1 (MQ=255)

                      aCGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCa                                                                                                           <  1:258035/139‑1 (MQ=255)

                           aTACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCGTGTCg                                                                                                      >  1:315086/1‑139 (MQ=255)

                              cccGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAg                                                                                                   <  2:557882/139‑1 (MQ=255)

                                        gATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCtgattgat                                                                                          <  1:148251/138‑1 (MQ=255)

                                                              aCAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACg                                                                    <  2:905/138‑1 (MQ=255)

                                                                    ctggctggATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATAGTGATTTGGCAGCCAATAACGGtggctg                                                             >  1:560101/1‑139 (MQ=255)

                                                                       ggtggATGCATAACAGGCGACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGCGATTTGGCAGCCAATAACGGtggctgg                                                            >  2:158394/3‑137 (MQ=255)

                                                                       gctggATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTgg                                                                                >  2:98080/1‑117 (MQ=255)

                                                                       gctggATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTgg                                                                                <  1:98080/117‑1 (MQ=255)

                                                                            aTGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCa                                                                              <  1:126785/114‑1 (MQ=255)

                                                                            aTGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCa                                                                              >  2:126785/1‑114 (MQ=255)

                                                                                 tAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCt                                                >  2:77705/1‑139 (MQ=255)

                                                                                      ggCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTgg                                                                                >  2:305634/1‑102 (MQ=255)

                                                                                      ggCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTgg                                                                                <  1:305634/102‑1 (MQ=255)

                                                                                       gCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGtggc                                                               >  2:284399/1‑118 (MQ=255)

                                                                                       gCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGtggc                                                               <  1:284399/118‑1 (MQ=255)

                                                                                       gCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAAcc                                          >  1:236803/1‑139 (MQ=255)

                                                                                         tACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCg                                                                                                      >  1:439108/1‑77 (MQ=255)

                                                                                         tACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCg                                                                                                      <  2:439108/77‑1 (MQ=255)

                                                                                         tACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAAcc                                          >  2:484415/1‑137 (MQ=255)

                                                                                         tACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAAcc                                          <  1:484415/137‑1 (MQ=255)

                                                                                           cGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGaa                                      >  2:501517/1‑139 (MQ=255)

                                                                                            ggATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCGTGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAAc                                     <  2:315086/139‑1 (MQ=255)

                                                                                                 atTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATg                                >  1:537653/1‑139 (MQ=255)

                                                                                                 atTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATg                                >  1:97124/1‑139 (MQ=255)

                                                                                                        ccAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGcc                         >  2:146449/1‑139 (MQ=255)

                                                                                                        ccAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGcc                         >  1:19833/1‑139 (MQ=255)

                                                                                                                      aaaGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCcgtattttcgtattt           >  1:394330/1‑139 (MQ=255)

                                                                                                                             tATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAAccc    >  1:572929/1‑139 (MQ=255)

                                                                                                                               ttGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCGa  <  2:236695/139‑1 (MQ=255)

                                                                                                                               ttGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCGa  <  2:236803/139‑1 (MQ=255)

ACAGGCCTGGCAGGAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGATCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCGA  >  NZ_CP009273/735904‑736169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `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

CCCGCACATTTACAGGCCTGGCAGGAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGATCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCG  >  NZ_CP009273/735893‑736168

CCAGCACATTTACAGGCCTGGCAGGAAGGCAAAACGGGGTACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGACAGATTTATTGTTCGACTGGC                                                                                                                               >  SRR3722139.527371/1‑151 (MQ=60)

                           GGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCGTGTCGC                                                                                                    >  SRR3722139.318979/1‑151 (MQ=60)

                                AACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTG                                                                                               <  SRR3722139.261285/151‑1 (MQ=60)

                                                  TGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGC                                                                              <  SRR3722139.150055/150‑1 (MQ=60)

                                                           gggctcggagatgtgtataagagacaGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAAC                                                                    <  SRR3722139.309423/125‑1 (MQ=60)

                                                            ataagagacagTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAAC                                                                    <  SRR3722139.99239/139‑1 (MQ=60)

                                                             gtgtataagagacagGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGG                                                                  <  SRR3722139.128345/136‑1 (MQ=60)

                                                                    GCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATAGTGATTTGGCAGCCAATAACGGTGGCTGG                                                           >  SRR3722139.566509/1‑151 (MQ=60)

                                                                            ataagagacaGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGTCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGC                                                   <  SRR3722139.287977/141‑1 (MQ=60)

                                                                                       ATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCG                                        >  SRR3722139.239732/1‑151 (MQ=60)

                                                                                         GCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGActgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatg                                      >  SRR3722139.444265/1‑99 (MQ=60)

                                                                                                 gtctcgtgggctcggagatgtgtataagagacagAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGC                              <  SRR3722139.118832/117‑1 (MQ=60)

                                                                                                 GGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGC                              <  SRR3722139.490056/151‑1 (MQ=60)

                                                                                                 GGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGC                              >  SRR3722139.543825/1‑151 (MQ=60)

                                                                                                 GGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGC                              >  SRR3722139.98273/1‑151 (MQ=60)

                                                                                                        GATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCG                       >  SRR3722139.20032/1‑151 (MQ=60)

                                                                                                                      GTTTTCTGGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTT         >  SRR3722139.399014/1‑151 (MQ=60)

                                                                                                                             GGTGAAAGATTTATTGTTCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCG  >  SRR3722139.579478/1‑151 (MQ=60)

CCCGCACATTTACAGGCCTGGCAGGAAGGCAAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATGCATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGATCGACTGGCGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAACGGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTCAACCCG  >  NZ_CP009273/735893‑736168

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`