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 F68 I1 R1	13	30.2	709236	94.0%	666681	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,018,557	G→T	S121* (TCA→TAA)	mgt ←	Monofunctional glycosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,018,557	0	G	T	100.0%	71.0 / NA	26	S121* (TCA→TAA)	mgt	Monofunctional glycosyltransferase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (12/14); total (12/14)

ATTGTTTTTCAACTCGATGAGCTACAAATAATTCTTTTACTTTTCTAGTAAATG‑AACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTT  >  USA300TCH1516_ALE/2018420‑2018688

atttgttttCAACTCGATGAGCTACAAATAATTTTTTTACTTTTCTAGTAAATGTTACTA‑CAATATAATTATGATAATTTTTGGCTACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTaaa                                                                                                                                  <  2:306583/136‑1 (MQ=255)

   gTTTTTCAACTCGATGAGCTACAAATAATTCTTTTACTTTTCTAGTAAATG‑AACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCTTTTAAAATa                                                                                                                               <  1:138057/141‑1 (MQ=255)

     ttttCAACTCGATGAGCTACAAATAATTCTTTTACTTTTCTAGTAAATG‑AACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATaaa                                                                                                                             >  1:237477/1‑141 (MQ=255)

                    gCTACAAATAATTCTTTTACTTTTCTAGTAAATG‑AACGATCATTATCCTCGCAATTATTTTTGACAACTTGCTGTGTAATAGTACTACCACCATGCACATCTCTGACGATACTCGTTTAAAATAAAGCTCTAGTTCTACCt                                                                                                              >  2:60201/1‑141 (MQ=255)

                     cTACAAATAATTCTTTTACTTTTCTAGTAAATG‑AACGATCATTATCATAAAACTAATTTTTGACAACTTGGTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATGTCGCTCGAGTTTTACCtt                                                                                                             >  2:248692/1‑141 (MQ=255)

                                          ttgtAGTAAATG‑AACTATCATTATCATAATAATAATTTTTGACAACTTGGTGTGTAATGGTACTACCACCTTGCACATCTCTGTAGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATgatgat                                                                                        <  2:112931/138‑1 (MQ=255)

                                            cTAGTAAATG‑AACGATCATTATCATAAAAATAATTTTTTTTTTTTTTTTTTATAATAGTACTACTACCTTTTACATTTTTTTTGCTTTTCGTTTAAAATAATGCTCTTCTTGTTCTTTTTTTATTTATTCCATGATGAttt                                                                                      >  2:247752/1‑140 (MQ=255)

                                                 aaaTG‑AACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGaa                                                                                 >  2:23256/1‑141 (MQ=255)

                                                 aaaTG‑AACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGaa                                                                                 <  1:49960/141‑1 (MQ=255)

                                                        aCGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTc                                                                           >  1:51997/1‑141 (MQ=255)

                                                         cGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACCTCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCa                                                                          >  1:205956/1‑141 (MQ=255)

                                                         cGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCa                                                                          >  1:67008/1‑141 (MQ=255)

                                                              aTTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTc                                                                     <  1:42137/141‑1 (MQ=255)

                                                                    aTAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGa                                                               >  1:239266/1‑141 (MQ=255)

                                                                    aTAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATAATAATTCAAGAATCGTTCATCTTCCATTGa                                                               >  2:87009/1‑141 (MQ=255)

                                                                    aTAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTAAACAAGTCTGTCGCTAGTCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGa                                                               >  1:152679/1‑141 (MQ=255)

                                                                                       aCTTGTTGTGTAATGGTACTCCCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCCAATCGAATCCATGATCATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTGAACa                                            <  1:99529/141‑1 (MQ=255)

                                                                                       aCTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCAGCTTCCATTGAAATAAAGGCACCTTTAACa                                            <  1:336434/141‑1 (MQ=255)

                                                                                             tgtgTAATGGTACTAACACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATActct                                      <  2:263349/141‑1 (MQ=255)

                                                                                                gtAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATACATGATGTTTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGc                                   <  2:345140/141‑1 (MQ=255)

                                                                                                        actacCACCTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATc                           <  1:243649/141‑1 (MQ=255)

                                                                                                            ccaccTTGCACATCTCTGTCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCt                       <  1:200374/141‑1 (MQ=255)

                                                                                                                              tCGCTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATCAACTCTCTTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTa     >  2:305143/1‑141 (MQ=255)

                                                                                                                                 cTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTAttt  <  1:287244/141‑1 (MQ=255)

                                                                                                                                 cTAATCGTTTAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTAttt  <  1:167643/141‑1 (MQ=255)

                                                                                                                                 atAATCGTTTAAAATAAAACTCTACTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCTTTCATCTTTCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTAttt  <  2:5469/140‑1 (MQ=255)

ATTGTTTTTCAACTCGATGAGCTACAAATAATTCTTTTACTTTTCTAGTAAATG‑AACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTT  >  USA300TCH1516_ALE/2018420‑2018688

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