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 F59 I0 R1	88	34.1	751148	93.4%	701572	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%	98.3 / NA	30	E175* (GAG→TAG)	USA300HOU_0930	possible HAD superfamily hydrolase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (17/13); total (17/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACCC  >  CP000730/973087‑973349

cGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCAt                                                                                                                            <  1:12653/141‑1 (MQ=255)

                     ggTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttt                                                                                                       <  2:259379/141‑1 (MQ=255)

                     ggTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttt                                                                                                       <  2:75225/141‑1 (MQ=255)

                              ttAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAg                                                                                              <  1:356063/141‑1 (MQ=255)

                               tAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAgg                                                                                             <  1:174661/141‑1 (MQ=255)

                               tAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAgg                                                                                             >  1:214848/1‑141 (MQ=255)

                                      tGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                      >  2:32147/1‑141 (MQ=255)

                                      tGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                      >  2:32137/1‑141 (MQ=255)

                                           aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttc                                                                                 <  2:334793/141‑1 (MQ=255)

                                                gCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCgg                                                                            >  1:308976/1‑141 (MQ=255)

                                                gCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCgg                                                                            >  1:308895/1‑141 (MQ=255)

                                                       gcttattgtgttattaATTACTAGTTTTCCAATTTCAATGACAGCGAACTGTGCGTTCTAGCGTCGATTCAAAATAAGATCGGGATAATAATTAGTGAGCTTAGTAATGATTTCAGGTATTTTACTTTCTTCGGCTTCAAt                                                                     <  2:216312/131‑1 (MQ=255)

                                                       gCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGATATTTTACTTTCTTGGACTTCAAt                                                                     >  2:130868/1‑141 (MQ=255)

                                                               cTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTg                                                             >  2:112888/1‑141 (MQ=255)

                                                                              gTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCtt                                              >  2:137437/1‑141 (MQ=255)

                                                                                 ttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCa                                           <  1:291093/141‑1 (MQ=255)

                                                                                 ttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAAGTAAAATTGAGGAAGGGGATTATTTCa                                           >  1:75139/1‑141 (MQ=255)

                                                                                 ttACAATTTCAATGAAAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCa                                           >  1:277406/1‑141 (MQ=255)

                                                                                  tACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCaa                                          >  2:65507/1‑141 (MQ=255)

                                                                                     aaTTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTg                                       >  2:75357/1‑141 (MQ=255)

                                                                                                cAGGGACTGGTGCGCCCCAGCGTCGGTGCTAAATATGATCGGCATAAAATTGAGCAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATGAATATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAAt                            <  2:127983/141‑1 (MQ=255)

                                                                                                cAGGGAATGGTGCGCTCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTATCAAGCTTCAATTAAAAATGAGGTAGGGAAGTCTTTCAAGTGGACACGTAAAt                            >  2:131145/1‑141 (MQ=255)

                                                                                                   ggAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTAc                         >  1:37255/1‑141 (MQ=255)

                                                                                                       tGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGt                     >  2:304930/1‑141 (MQ=255)

                                                                                                       tGGTGCGCCCCAGCATCGAGGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGt                     >  1:243484/1‑141 (MQ=255)

                                                                                                          tGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTg                  <  2:365699/141‑1 (MQ=255)

                                                                                                               cccAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTc             <  1:179180/141‑1 (MQ=255)

                                                                                                                ccAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGCTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCt            <  2:238175/141‑1 (MQ=255)

                                                                                                                    cGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGa        <  1:304930/141‑1 (MQ=255)

                                                                                                                          tGCTAAATATGATCGGCATCAAAATGAGTAAGCATATCTTTGATTTCAGGTATTTGACTTTCATCGGCTACAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTTGATTAccc  >  2:106870/1‑141 (MQ=255)

CGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACCC  >  CP000730/973087‑973349

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A