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	30	35.6	800162	95.7%	765755	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	100%	A155G (GCA→GGA)	ypdF ←	Aminopeptidase YpdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,646,189	0	G	C	100.0%	79.0 / NA	26	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (16/10); total (16/10)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATAT  >  USA300TCH1516_ALE/1646058‑1646322

cACTTGCAACCCCATATGGTAATGCAGCTCTATGTCCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTTTAATATTGCCTTTAATTCTTTTTGAGTCATGCCTCCTTTTacaa                                                                                                                              <  1:241966/141‑1 (MQ=255)

       aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaa                                                                                                                       >  1:334801/1‑141 (MQ=255)

       aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaa                                                                                                                       <  1:7762/141‑1 (MQ=255)

        acacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                                      >  2:205605/1‑141 (MQ=255)

           ccATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGCTGGTCCATCTGCTCATCATTCTAGTCTTTTGCTTTCTGATATTGGCTGTCGTTCTTTTTCAGTCATGCCTCCTTTTACAGCCGTTaaatat                                                                                                                   >  2:78256/1‑138 (MQ=255)

                 ggTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATTTCGCCTTGTACAACAGTTAAAATATATTCa                                                                                                             <  1:95152/141‑1 (MQ=255)

                       gCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGtt                                                                                                       >  2:227081/1‑141 (MQ=255)

                            tctATGACCAGATGCTACAATCGTATCGAATGATGGTCCAGCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcatc                                                                                                  <  1:282816/141‑1 (MQ=255)

                                            aCAATCGTATCGAATGATGGTACATCTGCTCCTAATTCTAGCATTTTGCTTTATAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTAATCAACAATATTAgctgct                                                                                  >  1:207729/1‑141 (MQ=255)

                                                             ttgTCCATCTGTTCCTGATTCTTGCGTTGTGCTTTTTATTATTGCCTTTTATTCTTTTTCAGTCATGCCTCCTTTTACATCAGTTTAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAt                                                                 <  2:75294/139‑1 (MQ=255)

                                                              ggTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTACTATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAtt                                                                >  2:114589/1‑141 (MQ=255)

                                                                 ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACACTATTAGCTGCTTTTTGAATTAAAGCAATTTCg                                                             >  2:353303/1‑141 (MQ=255)

                                                                   aTCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTGCAGTCATGCCTCCTTTTACAACCGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                           <  2:298125/141‑1 (MQ=255)

                                                                       gCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAACAATTTCGTCAGCa                                                       >  1:98827/1‑141 (MQ=255)

                                                                        cTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                                      >  1:398662/1‑141 (MQ=255)

                                                                                     cATTTTGCTTTCTAATATTGCCTTGAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTctct                                         <  1:1517/141‑1 (MQ=255)

                                                                                          tGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAGGTCTCTAAttt                                    >  1:235800/1‑141 (MQ=255)

                                                                                              ttCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAAGAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATc                                >  1:268664/1‑141 (MQ=255)

                                                                                               tCTAATAATGCCCTTAATTCTTTTTCAGTCATTCGTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCt                               <  2:72182/141‑1 (MQ=255)

                                                                                                cTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTa                              >  1:321835/1‑141 (MQ=255)

                                                                                                    tactGCTTTTTATTCTTTTTCAGTCATGCCTCCTTTTACAACACTTAAAATATATTCATATGTTTCATCAACAAAATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCACCTTTGACGTCTCTAATTTTATCTACAGt                          <  1:80718/138‑1 (MQ=255)

                                                                                                        gCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAttatta                      >  1:12683/1‑141 (MQ=255)

                                                                                                           tttAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGaa                   >  1:59380/1‑141 (MQ=255)

                                                                                                               aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc               <  1:227081/141‑1 (MQ=255)

                                                                                                                      ttCAGTCACGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATAAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTGGTCAGCATCTTTGACGTCTCTAAGTTTATCTACAGTATTAGAAATGCttattat        >  2:293738/1‑140 (MQ=255)

                                                                                                                            cATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTTATGttaa  >  2:196117/1‑140 (MQ=255)

CACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATAT  >  USA300TCH1516_ALE/1646058‑1646322

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