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
A12 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,956,875	G→A	515 (TAG→TAA)	ilvA →	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,956,875	0	G	A	100.0%	114.5 / NA	36	515 (TAG→TAA)	ilvA	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/20); total (16/20)

GACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAGGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACACACGCCCAGC  >  NC_000913/3956741‑3957008

gACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                                   >  2:476919/1‑139 (MQ=255)

  cTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaaaa                                                                                                                                 <  2:381738/139‑1 (MQ=255)

        gcgcGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTCGCGGGTTAAGGAAAAATGCCt                                                                                                                           >  2:883646/1‑139 (MQ=255)

           cgTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGAt                                                                                                                        >  1:570510/1‑139 (MQ=255)

                        ttCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTa                                                                                                           >  2:169394/1‑139 (MQ=255)

                          cGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATc                                                                                                         >  2:426700/1‑139 (MQ=255)

                                  gCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTAc                                                                                                 <  1:476919/139‑1 (MQ=255)

                                       cATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCcgcg                                                                                            <  2:608107/139‑1 (MQ=255)

                                                gATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATCGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGt                                                                                   >  1:948248/1‑139 (MQ=255)

                                                gATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAAc                                                                                     <  2:467394/137‑1 (MQ=255)

                                                gATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAAc                                                                                     >  1:467394/1‑137 (MQ=255)

                                                             ggCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCg                                                                      >  2:816780/1‑139 (MQ=255)

                                                                  aaTGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCaaa                                                                 <  1:883646/139‑1 (MQ=255)

                                                                            gCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGa                                                       <  1:482554/139‑1 (MQ=255)

                                                                                cGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGc                                                   <  1:816780/139‑1 (MQ=255)

                                                                                  aTTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCt                                                 <  1:426700/139‑1 (MQ=255)

                                                                                  aTTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCt                                                 <  2:948248/139‑1 (MQ=255)

                                                                                       cACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTG‑GGTTCGGCAAAATCTTCCAGAATGCCTCAATTa                                           <  1:169394/139‑1 (MQ=255)

                                                                                        acgacgAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTa                                           <  2:570510/139‑1 (MQ=255)

                                                                                                    aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                                    >  1:443161/1‑54 (MQ=255)

                                                                                                    aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                                    <  2:443161/54‑1 (MQ=255)

                                                                                                    aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                               >  1:38380/1‑59 (MQ=255)

                                                                                                    aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                               <  2:38380/59‑1 (MQ=255)

                                                                                                    aTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTa                               >  2:218767/1‑139 (MQ=255)

                                                                                                      aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaaaa                                                                                                                                 >  1:562961/1‑39 (MQ=38)

                                                                                                      aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaaaa                                                                                                                                 <  2:562961/39‑1 (MQ=255)

                                                                                                            gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                                    >  2:992584/1‑46 (MQ=255)

                                                                                                            gCGTTCAGGTTCTTTTTGGCGGGTTAACGAAAAATGCCTGATAgcg                                                                                                                    <  1:992584/46‑1 (MQ=38)

                                                                                                                   ggTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                          >  1:1360858/1‑49 (MQ=255)

                                                                                                                   ggTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                          <  2:1360858/49‑1 (MQ=255)

                                                                                                                   ggTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTgcg                <  2:991736/139‑1 (MQ=255)

                                                                                                                       cTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGcaca            <  1:218767/139‑1 (MQ=255)

                                                                                                                            tGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGcacac           <  2:423163/135‑1 (MQ=255)

                                                                                                                            tGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGcacac           >  1:423163/1‑135 (MQ=255)

                                                                                                                              gCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGaa                                                      <  2:1330806/90‑1 (MQ=255)

                                                                                                                              gCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGaa                                                      >  1:1330806/1‑90 (MQ=255)

                                                                                                                                 ggTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACACACGCCCAGc  >  1:1484611/1‑139 (MQ=255)

GACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAGGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACACACGCCCAGC  >  NC_000913/3956741‑3957008

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A