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 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	715,111	A→G	I269T (ATC→ACC)	speF ←	ornithine decarboxylase SpeF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	715,111	0	A	G	100.0%	94.5 / NA	27	I269T (ATC→ACC)	speF	ornithine decarboxylase SpeF
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (11/16); total (11/16)

CACAGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTT  >  NZ_CP009273/714985‑715238

cacaGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACg                                                                                                                       >  2:386140/1‑137 (MQ=255)

  caGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAgg                                                                                                                   <  1:42376/139‑1 (MQ=255)

    gATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGt                                                                                                                  >  2:271807/1‑138 (MQ=255)

        aCCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACt                                                                                                              <  1:271807/138‑1 (MQ=255)

         ccAATTTTATCCACCACTGGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACttt                                                                                                            <  2:241345/139‑1 (MQ=255)

            aTTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTttctt                                                                                                         <  1:287292/139‑1 (MQ=255)

                  tCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCaaaa                                                                                                    <  2:90908/138‑1 (MQ=255)

                  tCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAAGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCCGGTAACTTTCTTCaaaa                                                                                                    >  1:40052/1‑138 (MQ=255)

                      ccacTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTg                                                                                               <  1:386140/139‑1 (MQ=255)

                       cacTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTgc                                                                                              <  2:352152/139‑1 (MQ=255)

                                            cGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAg                                                                         >  2:342027/1‑139 (MQ=255)

                                                  gtcgtAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATAc                                                                   <  2:231225/139‑1 (MQ=255)

                                                   tcgtAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACg                                                                  >  1:418833/1‑139 (MQ=255)

                                                            ccTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTg                                                         <  2:157247/139‑1 (MQ=255)

                                                             cTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGc                                                        >  2:189694/1‑139 (MQ=255)

                                                                            cGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAAc                                         >  2:378853/1‑139 (MQ=255)

                                                                             gAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAAcc                                        <  2:356756/139‑1 (MQ=255)

                                                                                 cGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGgtg                                    <  1:83216/139‑1 (MQ=255)

                                                                                           gAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGcc                                                                                   >  2:255713/1‑82 (MQ=255)

                                                                                           gAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGcc                                                                                   <  1:255713/82‑1 (MQ=255)

                                                                                                           cTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCg          <  1:378853/139‑1 (MQ=255)

                                                                                                            tGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCgt         >  1:263561/1‑139 (MQ=255)

                                                                                                            tGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAAC‑TTCTTCAAAACAGTGCGCATCAATGCCACCGATa                                                                            <  2:27348/71‑1 (MQ=255)

                                                                                                            tGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAAC‑TTCTTCAAAACAGTGCGCATCAATGCCACCGATa                                                                            >  1:27348/1‑71 (MQ=255)

                                                                                                              cGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCgtg        <  1:23368/138‑1 (MQ=255)

                                                                                                                 tGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGtggtgg    >  1:195304/1‑139 (MQ=255)

                                                                                                                   cGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGtt  <  1:205825/139‑1 (MQ=255)

CACAGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTT  >  NZ_CP009273/714985‑715238

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `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

GAGTCAAACAGGATGTAGTCACACAGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGT  >  NZ_CP009273/714964‑715249

GAGTCAAACAGGATGTAGTCACACAGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTC                                                                                                                                          >  SRR3722119.166992/1‑150 (MQ=60)

                      ACAGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTC                                                                                                                   <  SRR3722119.42750/151‑1 (MQ=60)

                            GACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAAC                                                                                                              <  SRR3722119.274630/150‑1 (MQ=60)

                            GACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAAGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCCGGTAACTTTCTTCAAAAC                                                                                                              >  SRR3722119.40402/1‑150 (MQ=60)

                                AATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGC                                                                                                         <  SRR3722119.290251/151‑1 (MQ=60)

                                          CCCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGC                                                                                               <  SRR3722119.390021/151‑1 (MQ=60)

                                                      gatattcgccttagtctcgtgggctcggagatgtgtataagagacAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGC                                                                                   <  SRR3722119.258372/106‑1 (MQ=60)

                                                             AAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGG                                                                            >  SRR3722119.423043/1‑151 (MQ=60)

                                                                                                     GCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCC                                    <  SRR3722119.84019/151‑1 (MQ=60)

                                                                                                                      CTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTG                   >  SRR3722119.266284/1‑151 (MQ=60)

                                                                                                                      CTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAAC‑TTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtct                  >  SRR3722119.27592/1‑93 (MQ=60)

                                                                                                                           GCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGT              >  SRR3722119.197389/1‑151 (MQ=60)

                                                                                                                               GCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGA          <  SRR3722119.382666/151‑1 (MQ=60)

                                                                                                                                  GCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATT        <  SRR3722119.23581/150‑1 (MQ=60)

                                                                                                                                       GCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGT  <  SRR3722119.208034/151‑1 (MQ=60)

GAGTCAAACAGGATGTAGTCACACAGATGACCAATTTTATCCACCACTTGGCGGGCGTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGT  >  NZ_CP009273/714964‑715249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`