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
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,624,673	T→A	K192I (AAA→ATA)	malL ←	Oligo‑1,6‑glucosidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,624,673	0	T	A	100.0%	106.7 / NA	32	K192I (AAA→ATA)	malL	Oligo‑1,6‑glucosidase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (19/13); total (19/13)

GTAACCAAGTTTGTATACCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTTTATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATGTAGATCCATTA  >  USA300TCH1516_ALE/1624530‑1624813

gTAACCAAGTTTGTATACCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATc                                                                                                                                          >  3:276745/1‑148 (MQ=255)

gTAACCAAGTTTGTATACCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATc                                                                                                                                          >  4:254832/1‑148 (MQ=255)

gTAACCAAGTTTGTATACCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATc                                                                                                                                          >  3:27702/1‑148 (MQ=255)

     cAAGTTTGTATACCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAacc                                                                                                                                     <  3:239985/148‑1 (MQ=255)

              ataCCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTtca                                                                                                                            <  3:201614/148‑1 (MQ=255)

               taCCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTtcat                                                                                                                           <  4:345211/148‑1 (MQ=255)

                     acTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTc                                                                                                                     >  4:95950/2‑148 (MQ=255)

                      cTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCa                                                                                                                    <  3:158001/148‑1 (MQ=255)

                         aTTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATAGAAGCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAAt                                                                                                                 >  3:91945/1‑148 (MQ=255)

                               atCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCa                                                                                                           >  3:354670/1‑148 (MQ=255)

                                tCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAAt                                                                                                                 >  1:53133/1‑141 (MQ=255)

                                        aaaTGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACt                                                                                                  >  3:365062/1‑148 (MQ=255)

                                        aaaTGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACt                                                                                                  >  3:365058/1‑148 (MQ=255)

                                           tGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTcc                                                                                               <  3:152035/148‑1 (MQ=255)

                                           tGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTcc                                                                                               <  3:171045/148‑1 (MQ=255)

                                            gCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCg                                                                                              >  3:313570/1‑148 (MQ=255)

                                            gCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCg                                                                                              >  3:359789/1‑148 (MQ=255)

                                            gCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCg                                                                                              >  3:200505/1‑148 (MQ=255)

                                             cTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCgg                                                                                             <  3:287938/148‑1 (MQ=255)

                                                        gTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAAt                                                                                  <  3:118468/148‑1 (MQ=255)

                                                                    ggtacaggtaAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTGATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGgtt                                                                      >  3:300338/1‑148 (MQ=255)

                                                                       acaggtaAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGgttgtt                                                                   >  4:30002/1‑148 (MQ=255)

                                                                                                 cttcttAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAatat                                         >  4:55659/1‑148 (MQ=255)

                                                                                                 cttcttAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAatat                                         >  4:123584/1‑148 (MQ=255)

                                                                                                       aaTATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAataata                                          <  2:39608/141‑1 (MQ=255)

                                                                                                           tGCGTAATTGCATCTACTCTAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTAt                               <  4:25000/148‑1 (MQ=255)

                                                                                                                             ctAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATg             >  3:247610/1‑148 (MQ=255)

                                                                                                                             ctAAATCCATCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATAGAAATAATATTGATCAGTATTAGCATCatat                    >  2:57855/1‑141 (MQ=255)

                                                                                                                                  tCCATCAATGCCTATATCAAACCAACAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATGTAGAt        >  4:99706/1‑148 (MQ=255)

                                                                                                                                     aTCAATGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATGTAGATCCa     <  3:232917/148‑1 (MQ=255)

                                                                                                                                        aaTGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATGTAGATCCATTa  <  4:110680/148‑1 (MQ=255)

                                                                                                                                        aaTGCCTATATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATGTAGATCCATTa  <  4:344999/148‑1 (MQ=255)

GTAACCAAGTTTGTATACCTGGCTGATTCATATCTACATCAAATGCTGGGGCATATGTTTTACCCTCAGGTACAGGTAAGTCACCCGCTTCAAACGTCTTCTTAATATGCGTAATTGCATCTACTCTAAATCCATCAATGCCTTTATCAAACCACCAGTTCATCATTTCAAATACAGCATCTCTAACTTCCGGATTACCCCAATTCAAATCAGGTTGTTTTTTACTGAATAAATGGAAATAATATTGCTCAGTATTAGCATCATATTCCCATGTAGATCCATTA  >  USA300TCH1516_ALE/1624530‑1624813

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A