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
A21 F63 I0 R1	92	32.2	718920	92.2%	662844	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	973,213	C→A	100%	E175* (GAG→TAG)	USA300HOU_0930 ←	possible HAD superfamily hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	973,213	0	C	A	100.0%	83.4 / ‑6.5	29	E175* (GAG→TAG)	USA300HOU_0930	possible HAD superfamily hydrolase
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (15/13); total (16/13)
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.

ACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACC  >  CP000730/973085‑973348

aCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATCCCAAGTTTTACAATTTCAATGACAGGGAATGGTGGGCCCCAGCGTCGATGCTAAATATGATCGGc                                                                                                                             >  1:19126/1‑141 (MQ=255)

 ccctaTGCAATAATATTATTTCGGTCAATATTTAAAAATTGACTAACTTGCTCAATGCCACTTGCTCTATTAATCTCAAGCTTTACATTTTCAATGAAAGGGAGTGGTGCGCCGCTGCGTCGATGCTAAATATGATCGGCa                                                                                                                            <  2:116454/137‑1 (MQ=255)

 ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                            <  2:118679/141‑1 (MQ=255)

 ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                            <  1:167169/141‑1 (MQ=255)

         aataatATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATg                                                                                                                    >  1:230212/1‑141 (MQ=255)

          ataataTTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGa                                                                                                                   >  1:56392/1‑141 (MQ=255)

                  attTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCACCAGCGTCGATGCTAAATATGTTCGGCATAAAAATTAGTagacat                                                                                                           >  2:337338/1‑136 (MQ=255)

                   tttCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATAGGCATAAAAATGCGTAAGCata                                                                                                          >  2:248868/1‑141 (MQ=255)

                      cGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAttt                                                                                                       <  2:259069/141‑1 (MQ=255)

                      cGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAttt                                                                                                       <  2:20011/141‑1 (MQ=255)

                         tCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTCATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATCAAAATGATTAATCataatatgt                                                                                                    >  2:232040/1‑135 (MQ=255)

                                           cTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACtt                                                                                  >  1:210957/1‑141 (MQ=255)

                                                       aTGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCa                                                                      >  2:17048/1‑141 (MQ=255)

                                                         gCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAAt                                                                    >  1:220763/1‑141 (MQ=255)

                                                                   ttattaATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAg                                                          <  2:292316/141‑1 (MQ=255)

                                                                         aTACCAAGGTTTTCAATTTCAATGACAGGGAATGGTGCGCGCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAggg                                                    <  1:97917/141‑1 (MQ=255)

                                                                           aCCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGa                                                  >  1:348246/1‑141 (MQ=255)

                                                                              aaGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTc                                               <  1:49446/141‑1 (MQ=255)

                                                                              aaGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTc                                               <  1:298962/141‑1 (MQ=255)

                                                                               aGTTTTACAATTTCAATGACAGGGAATGGTGCGCACCAGAGTCGATGAAAAATGGTGTTTGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCt                                              <  1:10420/141‑1 (MQ=255)

                                                                                  tttACAATTTCAATGACCGGGGATGAGGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTc                                           >  2:77127/1‑141 (MQ=255)

                                                                                  tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATGTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTc                                           >  1:260081/1‑141 (MQ=255)

                                                                                               tGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTa                              <  2:325543/141‑1 (MQ=255)

                                                                                               tGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATACGAACGTCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTa                              <  1:97858/141‑1 (MQ=255)

                                                                                                         tGGTGCGCCCAAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGt                    <  1:313414/141‑1 (MQ=255)

                                                                                                          ggTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCTGtt                   >  2:67184/1‑141 (MQ=255)

                                                                                                                     gCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTgg        >  2:196933/1‑141 (MQ=255)

                                                                                                                         cGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTa    >  1:75629/1‑141 (MQ=255)

                                                                                                                           aTGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATCTCAGGAAGTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTATGGGATTCTTTCAAGTGGAAAAGTAAATTACCAGTTTGAATTCTTGGATTccc  >  2:21754/1‑141 (MQ=255)

ACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACC  >  CP000730/973085‑973348

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