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	965,365	T→C	M174T (ATG→ACG)	ycaQ →	winged helix DNA‑binding protein YcaQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	965,365	0	T	C	100.0%	100.5 / NA	29	M174T (ATG→ACG)	ycaQ	winged helix DNA‑binding protein YcaQ
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/16); total (13/16)

ATATTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGCC  >  NZ_CP009273/965239‑965499

atatTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACg                                                                                                                            >  2:560325/1‑139 (MQ=255)

  atTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGgc                                                                                                                          >  2:547950/1‑139 (MQ=255)

         aTAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACtt                                                                                                                   >  2:214891/1‑139 (MQ=255)

              gggCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAgc                                                                                                              <  2:281672/139‑1 (MQ=255)

              gggCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAgc                                                                                                              <  1:581216/139‑1 (MQ=255)

                    gTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGtt                                                                                                         >  2:7971/1‑138 (MQ=255)

                    gTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGtt                                                                                                         >  2:572472/1‑138 (MQ=255)

                              ccGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAAc                                                                                              >  1:111230/1‑139 (MQ=255)

                                        gCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTc                                                                                    <  1:214891/139‑1 (MQ=255)

                                                gTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAGCTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGa                                                                            <  1:547950/139‑1 (MQ=255)

                                                gTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGa                                                                            <  1:572472/139‑1 (MQ=255)

                                                       tGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGgat                                                                     >  2:345833/1‑139 (MQ=255)

                                                         cAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGgatga                                                                   >  2:459783/1‑139 (MQ=255)

                                                                              aGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGc                                               >  1:70019/1‑138 (MQ=255)

                                                                                 cGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAAc                                           <  2:330321/139‑1 (MQ=255)

                                                                                  gCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                          >  2:160048/1‑91 (MQ=255)

                                                                                  gCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                          <  1:160048/91‑1 (MQ=255)

                                                                                  gCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGCTTCGCaaa                                            >  2:489772/1‑137 (MQ=255)

                                                                                          ggCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGa                                  <  1:146002/139‑1 (MQ=255)

                                                                                              tCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAat                               >  1:521357/1‑138 (MQ=255)

                                                                                              tCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAat                               >  2:47812/1‑138 (MQ=255)

                                                                                                  gAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAAtcatca                          <  1:345833/139‑1 (MQ=255)

                                                                                                  gAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAAtcatca                          <  2:521357/139‑1 (MQ=255)

                                                                                                    aGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATg                        <  2:179587/139‑1 (MQ=255)

                                                                                                    aGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATg                        <  1:136514/139‑1 (MQ=255)

                                                                                                      gTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCt                      <  1:241814/139‑1 (MQ=255)

                                                                                                                     gAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGcgcg       <  1:7971/139‑1 (MQ=255)

                                                                                                                      aaaGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTTGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGcgcg       <  2:497702/138‑1 (MQ=255)

                                                                                                                      aaaGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGt      <  2:526353/139‑1 (MQ=255)

                                                                                                                          gtgacggtgatTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGcc  <  1:560325/139‑1 (MQ=255)

                                                                                                                          gtgacggtgatTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGcc  <  2:70019/139‑1 (MQ=255)

ATATTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGCC  >  NZ_CP009273/965239‑965499

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `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

GGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGCCTGGGAATATTC  >  NZ_CP009273/965252‑965510

GGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGAT                                                                                                              <  SRR3722139.587825/151‑1 (MQ=60)

      GGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACC                                                                                                        >  SRR3722139.112579/1‑151 (MQ=60)

                     acggtctcgtgggctcggagatgtgtataagagacaGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCC                                                                                          <  SRR3722139.162010/114‑1 (MQ=60)

                          AGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTG                                                                                    <  SRR3722139.217539/151‑1 (MQ=60)

                                  GGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAGCTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATG                                                                            <  SRR3722139.554248/151‑1 (MQ=60)

                                  CGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATG                                                                            <  SRR3722139.579017/151‑1 (MQ=60)

                                                      GTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCA                                                         >  SRR3722139.70841/1‑150 (MQ=60)

                                                                      CATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATC                                         >  SRR3722139.527369/1‑150 (MQ=60)

                                                                            CGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGC                                  <  SRR3722139.147779/151‑1 (MQ=60)

                                                                                    GGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAAC                          <  SRR3722139.350023/151‑1 (MQ=60)

                                                                                      AAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAG                        <  SRR3722139.138159/151‑1 (MQ=60)

                                                                                        GGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTG                      <  SRR3722139.244821/151‑1 (MQ=60)

                                                                                                       GGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGCCTGGGAA       <  SRR3722139.8047/151‑1 (MQ=60)

                                                                                                            GGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGCCTGGGAATATTC  <  SRR3722139.566734/151‑1 (MQ=60)

GGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCGTAGCCTGGGAATATTC  >  NZ_CP009273/965252‑965510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`