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 F41 I1 R1	11	26.2	606442	94.9%	575513	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,607	T→C	D22G (GAT→GGT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,607	0	T	C	100.0%	125.8 / NA	37	D22G (GAT→GGT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (25/12); total (25/12)

AAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATA  >  USA300TCH1516_ALE/1744470‑1744743

aaGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCt                                                                                                                                       <  2:106036/141‑1 (MQ=255)

     aCAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGaaa                                                                                                                                  <  1:290552/141‑1 (MQ=255)

                 aTGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGt                                                                                                                      >  1:193573/1‑141 (MQ=255)

                        aggcACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGcc                                                                                                               <  2:42168/138‑1 (MQ=255)

                         gCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCa                                                                                                              >  1:14139/1‑141 (MQ=255)

                                gcTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGa                                                                                                       >  2:183166/1‑141 (MQ=255)

                                           tACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTATCGCCTGGTTTCGGCCAATCTTGAACTTCTGATAc                                                                                            <  1:131486/141‑1 (MQ=255)

                                                  atatCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGc                                                                                     <  2:87548/141‑1 (MQ=255)

                                                  atagCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGc                                                                                     <  2:256061/141‑1 (MQ=255)

                                                    atCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCtt                                                                                   >  2:104379/1‑141 (MQ=255)

                                                     tCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTTACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCttt                                                                                  >  1:192698/1‑141 (MQ=255)

                                                      cAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTa                                                                                 >  1:138010/1‑141 (MQ=255)

                                                             tctGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCAt                                                                          >  2:290080/1‑141 (MQ=255)

                                                                gTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACTAATTGCTCTAAATCCATTaa                                                                       >  2:13559/1‑141 (MQ=255)

                                                                                    ttttATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTc                                                   >  2:169484/1‑141 (MQ=255)

                                                                                     tttATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCa                                                  >  1:215439/1‑141 (MQ=255)

                                                                                     tttATCTGTTGCATAGCCATATGCTTCACCATTATCCACAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCa                                                  >  1:237416/1‑141 (MQ=255)

                                                                                        aTCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTACGGCCAATCTTGAACTTCTGCTACGTATTGCTTTAAATCCATTCATATTTCCTCCTAAATTGCTCACgc                                               >  2:76359/1‑140 (MQ=255)

                                                                                         tgtggtGCATAGCCATATGCTTCAGCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTACTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGAc                                              <  2:200932/136‑1 (MQ=255)

                                                                                         tCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTTATGAc                                              >  2:188784/1‑141 (MQ=255)

                                                                                             ttGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAAtt                                          <  2:70247/141‑1 (MQ=255)

                                                                                             ttGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAAtt                                          <  1:119472/141‑1 (MQ=255)

                                                                                                 aTAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGa                                      >  1:259220/1‑141 (MQ=255)

                                                                                                  tAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGAc                                     >  2:60951/1‑141 (MQ=255)

                                                                                                  tAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAACTGTGAc                                     >  2:60956/1‑141 (MQ=255)

                                                                                                      cATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACtttt                                 >  2:198779/1‑140 (MQ=255)

                                                                                                        tatGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTAtt                               >  1:185951/1‑140 (MQ=255)

                                                                                                            cTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATGTTGGACTTCTGATACGTATGGCGGTGAGTCCGTTATTGTTGCCTCCGAAGTTTCTCTCGACATTGTTGATTTTATCGaag                           >  1:289046/1‑140 (MQ=255)

                                                                                                                      aTCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTc                 >  2:165915/1‑141 (MQ=255)

                                                                                                                       tCCATAATTGTAGTAATACCCTTGATACCGACAAATTCTTTCTGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTTACGACAATTGTTACTTTTTCCAATTTTTTATTTCt                >  2:66238/1‑141 (MQ=255)

                                                                                                                        ccATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTg               <  1:183166/141‑1 (MQ=255)

                                                                                                                         cATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATCAATCACGAGCTATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGa              >  1:222067/1‑141 (MQ=255)

                                                                                                                           tAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGaaa            <  2:65739/141‑1 (MQ=255)

                                                                                                                                gtagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCt       >  2:95888/1‑141 (MQ=255)

                                                                                                                                 tagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCtt      <  1:153897/141‑1 (MQ=255)

                                                                                                                                     aaTACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGatt  >  1:198576/1‑140 (MQ=255)

                                                                                                                                     aaTACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGata  >  1:137257/1‑141 (MQ=255)

AAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATA  >  USA300TCH1516_ALE/1744470‑1744743

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