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
A7 F184 I0 R1	35	35.7	768239	98.7%	758251	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,027,672	C→A	100%	G92V (GGC→GTC)	vraS ←	Sensor protein VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,027,672	0	C	A	100.0%	95.9 / ‑6.5	36	G92V (GGC→GTC)	vraS	Sensor protein VraS
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (23/12); minor base T (0/1); total (23/13)
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.

CATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACT  >  USA300TCH1516_ALE/2027538‑2027806

catTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTATATATTTTGATAATTAATGACAACt                                                                                                                                   >  1:719278/1‑140 (MQ=255)

catTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTATTGATTTAAAGGTACAAGTGTATGTTATAAATCTAACGTTTAACTATATATTTCTATATTTTGATAATTAATGACAACt                                                                                                                                   >  1:305765/1‑140 (MQ=255)

                   aTTGGTTAAGTTTTGAGTTTTACGTTGCAATTTATGCAATTCTGGATTTAAAGTTACAAGTGTTTGGTCTCCTGCCAACGTTTCGATTGATAACTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAAc                                                                                                                <  1:755534/140‑1 (MQ=255)

                                 gAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTc                                                                                                  >  1:447207/1‑140 (MQ=255)

                                           tCGCAACTTAATCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAAt                                                                                        <  1:47457/140‑1 (MQ=255)

                                             gCAACTTATGTAATTCTTGATTTAAAGTTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCa                                                                                      <  1:342053/140‑1 (MQ=255)

                                             gCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCTTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCa                                                                                      >  1:67813/1‑140 (MQ=255)

                                             gCAACTTAAGCAATTCTTGATTTAAAGGTACAAGTGTATTGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGAGCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCa                                                                                      <  1:342208/140‑1 (MQ=255)

                                                      gCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATTACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCtga                                                                             >  1:77757/1‑140 (MQ=255)

                                                                  ttAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTaa                                                                 >  1:534884/1‑140 (MQ=255)

                                                                       ggTACAAGCGTATTCTATAAATCTATCGTTTCATTATATATTTCTAGATTTTGATCATTAATGTCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATCTTGCTGATTGATTTTGTAAGCGAg                                                            <  1:77297/140‑1 (MQ=255)

                                                                         tACAAGTGTATGGTATAAATCTAACGTTTCACTATGTATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTTATTTTGTAAGCGAGTa                                                          <  1:424630/140‑1 (MQ=255)

                                                                         tACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTa                                                          <  1:99810/140‑1 (MQ=255)

                                                                            aaGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTTGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTACTGATTGATTTTGTAAGCGAGTACCg                                                       >  1:719411/1‑140 (MQ=255)

                                                                             agggtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGAGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGa                                                      >  1:63964/4‑140 (MQ=255)

                                                                             aGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGAACCGa                                                      >  1:368211/1‑140 (MQ=255)

                                                                                 tATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACca                                                  <  1:453830/140‑1 (MQ=255)

                                                                                   tGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTATTGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACcaac                                                <  1:421607/140‑1 (MQ=255)

                                                                                   tGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTTCTGATTGATTTTGTAAGCGAGTACCGAACcaac                                                <  1:108116/140‑1 (MQ=255)

                                                                                     gTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACcaacaa                                              <  1:701080/140‑1 (MQ=255)

                                                                                      tataAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATACAACTATGTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACaat                                             >  1:714682/1‑140 (MQ=255)

                                                                                       ataAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCCTTTTGCTTATTGATTTTGTAAGCGAGTACAGAAACAACaata                                            >  1:350638/1‑140 (MQ=255)

                                                                                       ataAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACaata                                            >  1:472510/1‑140 (MQ=255)

                                                                                       ataAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGAGTCTTAATCCAATCATTTTGCTGTTTGATTTTGTAAGCGAGTACCAAATCAACaata                                            >  1:110225/1‑140 (MQ=255)

                                                                                             cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGTACGCTCATTTTGCGTCTTAATACAATCATTTTGCTGATTGATTTTGTAAAGGAGTATCTATATAACAATAATgcac                                      >  1:27466/1‑140 (MQ=255)

                                                                                                    ttCAGTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAataata                               >  1:520343/1‑140 (MQ=255)

                                                                                                     tCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTACGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAatat                              >  1:81828/1‑140 (MQ=255)

                                                                                                             tttttCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATAtgatgatga                      <  1:705177/138‑1 (MQ=255)

                                                                                                                       ttttGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAAATGGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATAATGAGATTtaaaaa            >  1:335169/1‑140 (MQ=255)

                                                                                                                         ttGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaata          <  1:468926/140‑1 (MQ=255)

                                                                                                                           gATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATCTAATGATGAGATTtaaaaataaa        >  1:341642/1‑140 (MQ=255)

                                                                                                                            aTCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataaaa       >  1:546762/1‑140 (MQ=255)

                                                                                                                             tCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataaaaa      >  1:448296/1‑140 (MQ=255)

                                                                                                                             tCATTAAAGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTCATTGATTTTGTAAACGAGTACCGAACCAACAATAATACACAAAAATAAGATGATGAGATTtaaaaataaaaa      >  1:30267/1‑140 (MQ=255)

                                                                                                                              cATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATaaaaaa     >  1:598934/1‑140 (MQ=255)

                                                                                                                                 tAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCAAGTACCAAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACt  >  1:111693/1‑140 (MQ=255)

CATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACT  >  USA300TCH1516_ALE/2027538‑2027806

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A