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
A17 F109 I0 R1	32	27.2	584098	96.5%	563654	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	479,553	G→A	100%	A194T (GCA→ACA)	USA300HOU_0458 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	479,553	0	G	A	100.0%	74.8 / NA	26	A194T (GCA→ACA)	USA300HOU_0458	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (13/13); total (13/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479419‑479686

aTGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATgg                                                                                                                                  >  2:125644/1‑140 (MQ=255)

  gCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGtt                                                                                                                                <  1:194552/140‑1 (MQ=255)

    aataatAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGc                                                                                                                              <  1:27330/140‑1 (MQ=255)

        ataGATGAACAAGGTGAGCCACTTAGCGAAAAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAttt                                                                                                                          <  1:87932/140‑1 (MQ=255)

           gATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgc                                                                                                                       >  1:140219/1‑140 (MQ=255)

             tGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcgc                                                                                                                     <  2:28147/140‑1 (MQ=255)

              gAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCa                                                                                                                    <  2:164606/140‑1 (MQ=255)

                aCAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCAGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAAc                                                                                                                  >  1:225021/1‑140 (MQ=255)

                          ccACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAGTGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAg                                                                                                        >  2:93574/1‑140 (MQ=255)

                          ccACTTAGCGAACAAGAGAATCGTCAAATGATTAAATGGACGAAACTTAATATCGATGAATTTCTATCGAGTTGGACAATGCCGACGAATGAGCACATGTTGTAGCATACATGGTTGCATTTACAGCCACATGACAATAg                                                                                                        >  2:60625/1‑140 (MQ=255)

                                           gAATCGTCAAATGATTAAATGGACGAAACTTTATATATATCAAATTCTACAGTGTTATACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATTACCATAGTTTTACTTAATCACAgc                                                                                       >  1:68640/1‑140 (MQ=255)

                                             aacctCATATGACTAAATCGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAgcgc                                                                                     <  2:240060/136‑1 (MQ=255)

                                                 tCAAATGATTAAATGGACGAAACTTTATAACGATCGATTGCTATCGAGGTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                 <  1:49307/140‑1 (MQ=255)

                                                    aaTGATTAAATGAACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGGTGTACTCAAGCACAGCGCCAAGTGa                                                                              >  2:23622/1‑140 (MQ=255)

                                                          tAAATGGACGAAACTTTATATCGATCAATTTCTAGCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAg                                                                        <  1:118757/140‑1 (MQ=255)

                                                           aaaCGGGCGAAGCTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGGTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  1:77132/140‑1 (MQ=255)

                                                                         ttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATc                                                         >  2:58245/1‑140 (MQ=255)

                                                                             atCGATCAATTTATATAGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTAATATACATGGTTGCATTTAGCGCAACATGACCGTCGTTTTACTAAAACCCAGGGCCAAGTGATTAAAAGCTTcccctcggctactac                                                     >  2:45300/1‑129 (MQ=255)

                                                                                gATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGATCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAAt                                                  <  1:87204/140‑1 (MQ=255)

                                                                                          tATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATagag                                        >  1:281340/1‑140 (MQ=255)

                                                                                            tCGAGTTGGACAATGCGGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAATATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTc                                      <  2:225051/140‑1 (MQ=255)

                                                                                                            cGAAGCGTGAGCAAAGTTTGTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCAtttt                      <  2:209065/140‑1 (MQ=255)

                                                                                                             gAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCAttttt                     >  2:115071/1‑140 (MQ=255)

                                                                                                                      gCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAGTGACGATTGAGTTAGTATTAACTCATTTTTCTAtgggtg            >  1:133318/1‑135 (MQ=255)

                                                                                                                             ttttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGAGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTAAATAGATCAGGACGa     >  2:260027/1‑140 (MQ=255)

                                                                                                                                tACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTa  <  1:13639/140‑1 (MQ=255)

ATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479419‑479686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A