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 I0 R1	32	23.2	500348	95.1%	475830	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,758,882	G→A	71.8%	Q138* (CAA→TAA)	USA300HOU_1650 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,758,882	0	G	A	71.8%	42.2 / 18.9	32	Q138* (CAA→TAA)	USA300HOU_1650	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (2/7); new base A (14/9); total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-01

TTTGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATAA  >  CP000730/1758746‑1759013

tttGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCAtt                                                                                                                                 <  1:197339/141‑1 (MQ=255)

tttGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCAtt                                                                                                                                 <  2:218765/141‑1 (MQ=255)

       tACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATCTATTTCTTATGCCATAATTTCCTATGGATAACCATGTTCAGATGTTATTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAAtt                                                                                                                          >  1:111085/1‑141 (MQ=255)

       tACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGAAATATTTGCCTATTGATAAGCATGTTCATAGTCTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAAtt                                                                                                                          >  1:111078/1‑141 (MQ=255)

            cAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTa                                                                                                                     <  1:172735/141‑1 (MQ=255)

            cAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTa                                                                                                                     <  1:186574/141‑1 (MQ=255)

             aaCCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTAt                                                                                                                    >  1:96958/1‑141 (MQ=255)

                 ttttAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTa                                                                                                                <  2:194161/141‑1 (MQ=255)

                 ctttAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTa                                                                                                                <  2:34828/140‑1 (MQ=255)

                      aaTTTATTCTTGTGGCCGGATAACTAAAAGATATTTCTTATGCAAGATTTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTTCCGTGTTTTAGTTAAGTCTTGTTGCATTACGAATTCAGTACTGTAAtcac                                                                                                           <  2:160751/141‑1 (MQ=255)

                        tttATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGc                                                                                                         >  2:62227/1‑141 (MQ=255)

                          tATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCAt                                                                                                       >  2:32450/1‑141 (MQ=255)

                          tATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCAt                                                                                                       >  1:15613/1‑141 (MQ=255)

                                         aTAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCaaa                                                                                        <  1:14485/141‑1 (MQ=255)

                                           aaCTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCaaagt                                                                                      >  1:44774/1‑139 (MQ=255)

                                           aaCTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAAtt                                                                                      >  2:248544/1‑141 (MQ=255)

                                                                    aatTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCctct                                                             <  1:32450/141‑1 (MQ=255)

                                                                           tATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCt                                                      <  2:130919/141‑1 (MQ=255)

                                                                             ttGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGCCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCtat                                                    <  2:96958/141‑1 (MQ=255)

                                                                                 gaaGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTataata                                                <  2:245987/140‑1 (MQ=255)

                                                                                   aGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCAAATTAGTCGTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAatata                                              >  1:48736/1‑141 (MQ=255)

                                                                                     cATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCGCTTTGACCTATAATATAtt                                            <  1:62227/141‑1 (MQ=255)

                                                                                      agcttCAGCGTTTAGTTGTAAATTTTGCCCTAATTCATATAAGACCTTGTACATTTCAACATCAGTATTGTAAACACCCGTTGAATCATCTCCCAATTTATAAATAATAAATTCGTCGCCTCTCTTGCCTATAATAAATTg                                           >  2:15067/4‑141 (MQ=255)

                                                                                        tttCAGATTTTAGTTGTAAATTTTGCCCTACTTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCGAACTTTATAAAGAATAAATTCGTCTCCTCTTTCACCTATAATATATTGAt                                         <  2:183475/141‑1 (MQ=255)

                                                                                                  tAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGc                               >  1:220221/1‑141 (MQ=255)

                                                                                                       gTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGTTCATTATAAGCCATGc                          >  1:160090/1‑141 (MQ=255)

                                                                                                        tAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCg                         <  1:189859/141‑1 (MQ=255)

                                                                                                              ttGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGattcat                   >  2:57043/1‑141 (MQ=255)

                                                                                                              ttGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGattcat                   >  2:56874/1‑141 (MQ=255)

                                                                                                                    tAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGa             <  2:12990/141‑1 (MQ=255)

                                                                                                                               aGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGCCTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATACAATTCATTCCAACCACCGCCAtca  >  2:197930/1‑139 (MQ=255)

                                                                                                                               aGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATACTATATTGATCATTATAAGCCATGCGATTCATTCCAAACACACCCATaa  >  2:156921/1‑141 (MQ=255)

TTTGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATAA  >  CP000730/1758746‑1759013

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