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 F172 I0 R1	42	33.2	716278	96.8%	693357	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%	121.3 / ‑6.5	38	A194T (GCA→ACA)	USA300HOU_0458	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (15/22); minor base C (0/1); total (15/23)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479420‑479686

tGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGt                                                                                                                                 <  2:200495/140‑1 (MQ=255)

 gCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGtt                                                                                                                                <  1:235280/140‑1 (MQ=255)

 gCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGtt                                                                                                                                <  1:166810/140‑1 (MQ=255)

     taataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAACGATTTTACCATACATGGTTGCAt                                                                                                                            >  2:148922/1‑140 (MQ=255)

     taataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAt                                                                                                                            >  1:277374/1‑140 (MQ=255)

     taataGATGAACAAGGTGAGCCACGTAGCCAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAt                                                                                                                            <  2:274439/140‑1 (MQ=255)

      aataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAtt                                                                                                                           <  1:141426/140‑1 (MQ=255)

       ataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAttt                                                                                                                          <  2:220740/140‑1 (MQ=255)

          gATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgc                                                                                                                       <  2:296177/140‑1 (MQ=255)

           aTGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcg                                                                                                                      >  1:201017/1‑140 (MQ=255)

                    gTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACTATACATGGTTGCATTTAGCGCAACATGAc                                                                                                             >  1:51629/1‑140 (MQ=255)

                    gTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGAc                                                                                                             <  1:339370/140‑1 (MQ=255)

                      gAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCa                                                                                                           >  2:122069/1‑140 (MQ=255)

                        gCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCTCAACATGACCATa                                                                                                         >  2:108159/1‑140 (MQ=255)

                                gctaaCAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACt                                                                                                 <  1:139502/137‑1 (MQ=255)

                                 cGAACAAGTGAATCGTCAAATGATTAAATGGACGAATCTTTATATTTAGCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTa                                                                                                <  1:274950/140‑1 (MQ=255)

                                  gAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGCTTTACTaa                                                                                               <  1:312185/140‑1 (MQ=255)

                                  gAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACACGGTTGCATTTAGCGCAACATGACCATAGTTTTACTaa                                                                                               <  2:136532/140‑1 (MQ=255)

                                           aaTCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTATTACTAAAGCACAgcg                                                                                      >  1:34744/1‑140 (MQ=255)

                                                   aaTGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATATTTTTACTAAAGCACAGCGCCAAGTGa                                                                              <  2:163331/140‑1 (MQ=255)

                                                     tGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACCGCGCCAAGTGAtt                                                                            <  2:356453/140‑1 (MQ=255)

                                                          aaaTGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  1:207019/140‑1 (MQ=255)

                                                          aaaTCGACGAAACCTTATATCCATCAATTTCTATCGAGTTGGACAAGGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  2:177108/140‑1 (MQ=255)

                                                           aaTGGACGAAACTTTATATCGATCAATTTCTATCGCGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAACTGATTAAAGGc                                                                      >  1:133896/1‑140 (MQ=255)

                                                            aTGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGCAACGACAGCAAATTTTTTACCATACATAGTTGCATATAGCACAACAGGACCCTAGTTTTGTTAAAGCACAGCGGGCACTGAATAAAGGCt                                                                     >  2:245811/1‑140 (MQ=255)

                                                                     accttATTTCGATAAATTCTTAAGAAGATGGACAATGACGAAGCGTGACCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGATTTACTAAAGCACAGCGCCAAGTGATTAGAGGCTTCACCAAtc                                                            >  2:253395/4‑139 (MQ=255)

                                                                     aatttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATg                                                            <  2:239510/138‑1 (MQ=255)

                                                                     aCTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATg                                                            <  1:356128/140‑1 (MQ=255)

                                                                       tttATATCGATCAATCTCTATCGAGCTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGAt                                                          >  1:178970/1‑140 (MQ=255)

                                                                          atatCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCt                                                       <  2:237210/140‑1 (MQ=255)

                                                                            acagatcaagtatgaTCGAGTTGGACAATGCCGAAGCGTGTCTAAACTTATTCCCACACATGGGTACATTCAGAACAAACCCCCCTTACTGTTACGAAAGCACAACTCCTAGTGATTAAAGTCTTTCCCAATTATTCTGa                                                     <  2:109389/126‑1 (MQ=255)

                                                                             tCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGaa                                                    <  1:163516/140‑1 (MQ=255)

                                                                                    aTTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGa                                             <  2:5972/140‑1 (MQ=255)

                                                                                                  ggACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGGGCAAAGAAAATAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTa                               >  1:67414/1‑140 (MQ=255)

                                                                                                  ggACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTa                               >  1:286314/1‑140 (MQ=255)

                                                                                                                 gTGAGCCAATTTTCTACCATCCATGGTGGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATa                <  2:272341/140‑1 (MQ=255)

                                                                                                                        aaGTTTTTACCATACATGATTGCATTTAGCGCAACATGACCAGAGTGGTACTAAAGCACAGAGCGAAGTGATTAAAGGCTTACGCAAGGAGCGTGAAATGACGATAGAGTAAGTATTAACTCATTTTTCAATAGATCAgg         >  2:120025/1‑140 (MQ=255)

                                                                                                                               tACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTTATTTTTCAATAGATCAGGAAGACTa  >  1:294130/1‑140 (MQ=255)

TGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479420‑479686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A