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
A13 F40 I1 R1	12	34.5	773110	93.2%	720538	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,513,930	0	A	T	100.0%	87.1 / NA	25	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (11/14); total (11/14)

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAAAATG  >  USA300TCH1516_ALE/1513796‑1514070

ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGGCTCTTGGATAAAGAGTACAAAAAATACTGCTAGAAATGTACCACATCGCGTAAAAGATCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                                 <  1:223131/148‑1 (MQ=255)

 tatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                                <  2:256070/148‑1 (MQ=255)

 tatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACAAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                                <  2:193629/148‑1 (MQ=255)

  atttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATTTATATCACTCATAATATGTTTTATTGTATTAGGatta                                                                                                                               <  2:347241/148‑1 (MQ=255)

     tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGAttatta                                                                                                                            <  2:59544/148‑1 (MQ=255)

       tatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                          <  2:38126/148‑1 (MQ=255)

               gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCCCTCATAATCTGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                                  <  1:342214/148‑1 (MQ=255)

                           gCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGCACAAAAAATACTGCAATAAAACTACCACATCGCGTCACAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTCGATTATAAc                                                                                                      >  2:325820/1‑148 (MQ=255)

                               ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                                  >  2:258384/1‑148 (MQ=255)

                                        ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                         >  1:119832/1‑148 (MQ=255)

                                                 ctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                                >  2:85087/1‑148 (MQ=255)

                                                       tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                                          >  2:294715/1‑148 (MQ=255)

                                                           gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                      <  1:375241/148‑1 (MQ=255)

                                                             gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                                                    >  2:355446/1‑148 (MQ=255)

                                                                  aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                               <  2:257052/148‑1 (MQ=255)

                                                                  aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                               <  1:49471/148‑1 (MQ=255)

                                                                   aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTACTGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                              <  1:233170/148‑1 (MQ=255)

                                                                   aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTACCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                              <  1:301482/148‑1 (MQ=255)

                                                                               tAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                                  >  1:199243/1‑148 (MQ=255)

                                                                                         acaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                                        >  2:385541/1‑148 (MQ=255)

                                                                                         acaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                                        >  2:75603/1‑148 (MQ=255)

                                                                                            tCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGc                                     <  2:119832/148‑1 (MQ=255)

                                                                                                             cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACt                    <  1:149894/148‑1 (MQ=255)

                                                                                                                     tCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt            >  1:88569/1‑148 (MQ=255)

                                                                                                                               tatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAAAATg  >  2:107476/1‑148 (MQ=255)

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAAAATG  >  USA300TCH1516_ALE/1513796‑1514070

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A