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
A19 F57 I0 R1	85	36.1	800162	93.0%	744150	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%	92.4 / NA	30	E175* (GAG→TAG)	USA300HOU_0930	possible HAD superfamily hydrolase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (18/12); total (18/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAC  >  CP000730/973077‑973347

tCTTCATGACCGAATGCAATATTATTATTTCGGTAAATCTTTAGAAATTGTCTAGCTAGCTCAATGCATCTTTCTTTATTAATACCAAGTTTTACCATTTCGCTGACAGGGCGTGTTGCACCCCAGAGTCGCTGCTAAata                                                                                                                                    >  2:300124/1‑141 (MQ=255)

         ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                           >  1:351300/1‑141 (MQ=255)

               tcAATAATATTTTTTCGGTCAATATTTAAAAAGTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCTGCGTCGATGCTAAATATGATCGGCATaaaaa                                                                                                                     <  2:117013/140‑1 (MQ=255)

               gCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaatta                                                                                                                     >  2:398402/1‑138 (MQ=255)

                   taataTTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCTATTCCGCTTTCTTTATTCATACGAAGTTTTACATTTTCAATGACAGGGAATGGTGCGCCCCAGCGGCGATGCTAAATATGATCGGCATAAAAATGAg                                                                                                                 <  2:141983/141‑1 (MQ=255)

                       attattTCGGTCAATATTTACAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAg                                                                                                             <  2:301721/141‑1 (MQ=255)

                       attattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAg                                                                                                             <  2:172427/141‑1 (MQ=255)

                       attattTCGGTCAATATTTAAAAATTGTCTAACTTACTCAATGCCACTTTCCTTAATAATACCAACGGTTACAATTTCAATGACATTGAATGTTGCGCCCCAGCTTCGATGCTAAATATGATCGGCATAAAAATGAGTAAg                                                                                                             <  2:231144/141‑1 (MQ=255)

                         tattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCa                                                                                                           <  1:134423/141‑1 (MQ=255)

                         tattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGACTCTTGCTCTATTAATACCTAGTTGTACAATTTCCATGCATGGTGAGGACCCGCCCCAGCGGCGATACGAAATATGATCGGCATAAAAAGGAGTAAGCa                                                                                                           >  2:382855/1‑141 (MQ=255)

                           tttCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCata                                                                                                         >  1:229734/1‑141 (MQ=255)

                                  cAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttttaa                                                                                                  >  2:39579/1‑139 (MQ=255)

                                   aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCTTCGATGCTAAATATGATCGGCATAAAAATCAGTAAGCATATTTTTGAt                                                                                                 >  2:73645/1‑141 (MQ=255)

                                   aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAt                                                                                                 <  1:178583/141‑1 (MQ=255)

                                        ttcaataTTGTCTTACTTGCTCAATGCCTCTGGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAg                                                                                            <  2:80996/135‑1 (MQ=255)

                                                tGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATCTGACCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                    <  1:77589/141‑1 (MQ=255)

                                                tGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTAAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                    >  1:133114/1‑141 (MQ=255)

                                                     aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttc                                                                               >  1:21851/1‑141 (MQ=255)

                                                      aCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttct                                                                              >  2:116694/1‑141 (MQ=255)

                                                      aCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttct                                                                              >  2:173015/1‑141 (MQ=255)

                                                           cTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAAAGCGTGAGATTTTTTTTGATTTCAGGTATTTTACTTTCTTCGGc                                                                         >  1:372039/1‑141 (MQ=255)

                                                                 gCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAAt                                                                   <  2:68206/141‑1 (MQ=255)

                                                                        gCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAAtt                                                            >  1:330508/1‑141 (MQ=255)

                                                                          tttATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCCTAAAAATGAGTATGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGTCTTCCATTTATATTgg                                                          >  2:39334/1‑140 (MQ=255)

                                                                                 aTACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTGCAATTAAAATTGAGGTAggt                                                   <  2:134820/141‑2 (MQ=255)

                                                                                        gTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCtt                                            <  1:375549/141‑1 (MQ=255)

                                                                                         ttttACAATTTCAATGACAGGGAATGGTGCGCCCCAGAGTCGGTGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTTTTCGGCTTCAATTAAAGTTGAGGAGGGGGTTTCttt                                           >  1:112880/1‑141 (MQ=255)

                                                                                             aCAATTTCAATGACAGAGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAg                                       >  1:198038/1‑141 (MQ=255)

                                                                                                         aCAGGGAATGGTGCGCCCCAACGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTaaa                           >  1:319928/1‑141 (MQ=255)

                                                                                                                                  gATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAc  >  1:36863/1‑141 (MQ=255)

TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAC  >  CP000730/973077‑973347

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