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
A3 F75 I1 R1	13	22.6	534182	93.9%	501596	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,372,751	A→T	L342* (TTA→TAA)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,372,751	0	A	T	100.0%	75.3 / NA	29	L342* (TTA→TAA)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (18/11); total (18/11)

CACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCT  >  USA300TCH1516_ALE/2372621‑2372885

cACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTCACGGACTAAAGAACAGCGCATATAGGAaac                                                                                                                               >  2:72951/1‑140 (MQ=255)

  cTGCAACTTCGAAACTTTTCCAGTTTTTCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACACCGATTAACGGACTAAAGACCCGCGCTTATAGGAaacaa                                                                                                                             >  2:110048/1‑140 (MQ=255)

  cTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACCGCGCTTATAGCAaacac                                                                                                                             >  2:9827/1‑139 (MQ=255)

              aaCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACg                                                                                                                 >  2:180443/1‑140 (MQ=255)

                  tttCCAGTTTATCTCAGCAAAGTTTGCAGCAATTAATACACCTAACACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAACGCTTATAACAAACAAAAACCTGTTaacacac                                                                                                             >  2:260249/1‑134 (MQ=255)

                      cAGTTTATCTCAGCAAGGTTTGCAGCCATTAATACACCTACCACCACTAGGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGc                                                                                                         <  2:142980/140‑1 (MQ=255)

                      cAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAATGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGc                                                                                                         <  2:212583/140‑1 (MQ=255)

                            aTCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATcc                                                                                                   >  1:4869/1‑140 (MQ=255)

                               tcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTTTTACAACAGTGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGt                                                                                                <  1:230628/140‑1 (MQ=255)

                               tcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGt                                                                                                >  1:132585/1‑140 (MQ=255)

                               tcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGt                                                                                                <  1:27220/140‑1 (MQ=255)

                                     aaGTCTGCATCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATATGAAACAACATCCTGTTACGATACTAGCAAATCCTGTTCTAGc                                                                                          <  2:90766/140‑1 (MQ=255)

                                             aGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAg                                                                                  <  1:145540/140‑1 (MQ=255)

                                                cATTAATACACCTACTACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCCACTTACAGTCTATATAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCaa                                                                               <  2:230859/140‑1 (MQ=255)

                                                 aTTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAac                                                                              <  1:94143/140‑1 (MQ=255)

                                                         acCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAg                                                                      <  1:180443/140‑1 (MQ=255)

                                                                accacTAAGGCTGGTGTCGTAACTGCACTTGTTCCAACAACGATTAACGCACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCCTCTACAGCAACACCTGAAGTTGATTc                                                               >  1:51672/1‑140 (MQ=255)

                                                                               gtCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTCGATTCGATATAAGACattgt                                                >  2:139422/1‑140 (MQ=255)

                                                                               gtCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAAACAACTGTTACGATAATAGCAAAACCTACTCAAACACCTACAGCAACACCTGAAATTGAGTCGCAAAaagaaagagt                                                >  2:132420/1‑135 (MQ=255)

                                                                                 cGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACAGCGGAAGTTGATTCGCCCTCAGAAGttgttg                                              <  2:110063/140‑1 (MQ=255)

                                                                                 cGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCCATATAAGCAGttggtg                                              >  1:266725/1‑140 (MQ=255)

                                                                                           cTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTAGTAGTTGTTcc                                    >  2:208517/1‑140 (MQ=255)

                                                                                              gTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAAGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGAAACTACAGCACCACCTGAAGTTGATTAGATATAAGAACTTGTTGTAGTTGTTcacaa                                 >  2:56811/1‑136 (MQ=255)

                                                                                              gTTACAACAGCGAATAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACGAGCAAATCCTGTTCTAACACCTACAGCAACACCTAAAGTTGATTCGATATAATAAATAGTTGTAGTTGTTCaaaa                                 >  2:23029/1‑140 (MQ=255)

                                                                                                  caacaGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACt                             >  2:249560/1‑140 (MQ=255)

                                                                                                                      aaGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAATTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaa         >  1:171051/1‑140 (MQ=255)

                                                                                                                       aGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaaa        <  1:226152/140‑1 (MQ=255)

                                                                                                                       aGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaaa        >  1:158050/1‑140 (MQ=255)

                                                                                                                             gcgcTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTCGATTCCATATAAGAAGTTGTCGTAGTTATTCAAAAAACTGCTCCCACAAACATCGCTAAAGAATCt  >  2:55260/1‑140 (MQ=255)

CACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCT  >  USA300TCH1516_ALE/2372621‑2372885

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