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
A23 F110 I1 R1	27	27.0	575272	98.6%	567218	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,758,882	G→A	Q138* (CAA→TAA)	USA300HOU_RS08780 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,758,882	0	G	A	100.0%	104.9 / NA	29	Q138* (CAA→TAA)	USA300HOU_RS08780	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/15); total (14/15)

TTTGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATAA  >  USA300TCH1516_ALE/1758746‑1759013

tttGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACAtt                                                                                                                                 >  2:195063/1‑141 (MQ=255)

 ttGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACAttt                                                                                                                                >  2:287166/1‑141 (MQ=255)

    aaCTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCaa                                                                                                                             >  1:64096/1‑141 (MQ=255)

              aCCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGCTAAGCATTTTCAGATTTTAGTTGTACAATTTCCCTTGCTTCATTTAAGTCTTGTTACATTTCAAATTCAGTAtt                                                                                                                   >  1:2621/1‑141 (MQ=255)

               ccTTTTAAATTTATTCTAGTGACAGGATAACTAAAATTTATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTg                                                                                                                  <  2:208145/141‑1 (MQ=255)

               ccTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTg                                                                                                                  <  1:199256/141‑1 (MQ=255)

                                        gATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCaa                                                                                         <  2:95192/141‑1 (MQ=255)

                                            aCTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAAttt                                                                                     >  1:158902/1‑141 (MQ=255)

                                            aCTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAAttt                                                                                     >  2:205453/1‑141 (MQ=255)

                                                    atatTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGaa                                                                             <  2:64096/141‑1 (MQ=255)

                                                       tttCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATaa                                                                          >  1:24870/1‑141 (MQ=255)

                                                         tCTTATGCAATAATGTCCTATTCGAAAGCAAATTCATATTTAATTTGGAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAAt                                                                        <  1:83289/141‑1 (MQ=255)

                                                               gCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGtct                                                                  <  1:235827/141‑1 (MQ=255)

                                                               gCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGtct                                                                  <  1:50442/141‑1 (MQ=255)

                                                                   taatTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTctcctc                                                              <  1:253334/141‑1 (MQ=255)

                                                                   taatTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTctcctc                                                              <  2:226768/141‑1 (MQ=255)

                                                                          cTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGAcc                                                       >  1:53442/1‑141 (MQ=255)

                                                                          cTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCACTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGAcc                                                       >  2:247551/1‑141 (MQ=255)

                                                                                 tAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATATTCAATCTGATAAAGAATAAATTCGTCTCCTCTTTGACCTataata                                                <  1:209834/141‑1 (MQ=255)

                                                                                  aaGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAatat                                               <  1:9356/141‑1 (MQ=255)

                                                                                        tttCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGAt                                         >  1:1736/1‑141 (MQ=255)

                                                                                         ttCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATc                                        <  2:158902/141‑1 (MQ=255)

                                                                                         ttCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATc                                        <  1:205453/141‑1 (MQ=255)

                                                                                           cAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTTACGCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCAt                                      >  1:56805/1‑141 (MQ=255)

                                                                                           cAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCAt                                      >  1:65197/1‑141 (MQ=255)

                                                                                                 ttttttGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGTCTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAg                                >  2:213579/5‑141 (MQ=255)

                                                                                                                             tAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCAt    <  1:195063/141‑1 (MQ=255)

                                                                                                                              aaGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATa   <  1:287166/141‑1 (MQ=255)

                                                                                                                               aGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATaa  >  2:255330/1‑141 (MQ=255)

TTTGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATAA  >  USA300TCH1516_ALE/1758746‑1759013

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

GATK/CNVnator alignment

N/A