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
A23 F43 I0 R1	23	38.0	846132	95.3%	806363	140.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,450	A→T	32.1%	F74L (TTT→TTA)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,450	0	A	T	32.1%	49.6 / 34.0	44	F74L (TTT→TTA)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base A (19/10); new base T (8/6); total (28/16)
Fisher's exact test for biased strand distribution p-value = 7.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

CTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATAT  >  USA300TCH1516_ALE/1744320‑1744576

cTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcc                                                                                                                      <  2:171885/141‑1 (MQ=255)

cTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTATAACAGGTGCTAAGCCAATcc                                                                                                                      >  1:354602/1‑141 (MQ=255)

cTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATcc                                                                                                                      >  1:228883/1‑141 (MQ=255)

             acGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGc                                                                                                         <  2:402665/141‑1 (MQ=255)

               gTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACAAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCCAAGCCAATCCCCCTTCAAAAATCtc                                                                                                       >  2:38225/1‑140 (MQ=255)

                  gACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAg                                                                                                    >  2:160951/1‑141 (MQ=255)

                    ccTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGa                                                                                                  <  1:244817/141‑1 (MQ=255)

                     ttGGTGTAATTGCATCGTTGTGGATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGAc                                                                                                 <  2:114456/140‑1 (MQ=255)

                       ggTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAg                                                                                               <  2:15882/141‑1 (MQ=255)

                           tAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACATGACAGccca                                                                                           >  1:392332/1‑139 (MQ=255)

                             aTTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAAGGTCATACGGCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATg                                                                                         <  1:199019/141‑1 (MQ=255)

                             aTTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATTAGCTACAGGACAGCCAATg                                                                                         >  1:233695/1‑141 (MQ=255)

                             aTTGCATCTTTGTGCATTGTTAAAAACTATCAAACCTATGCGAGGTCATACTTATAACGAATGACTTCACGAGGTAATTCACCTTCTTTTCTAACACATTCAAAGCCAAACACCATTAAATAATCTACAGTACAGACaaaa                                                                                         >  2:92179/1‑139 (MQ=255)

                              ttGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGa                                                                                        >  1:106707/1‑141 (MQ=255)

                              ttGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGa                                                                                        >  1:203517/1‑141 (MQ=255)

                                 cATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATCATaa                                                                                     >  2:204245/1‑141 (MQ=255)

                                 cATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATaa                                                                                     >  1:184581/1‑141 (MQ=255)

                                   tCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGCTGCTAAGCAAATCCCCATTGAATAAGCTACAGGACAGCCAACGATaaaa                                                                                   >  2:317883/1‑140 (MQ=255)

                                        gtgCATTGGTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAAGGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcg                                                                              <  2:411987/141‑1 (MQ=255)

                                         tgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcgc                                                                             <  1:236876/141‑1 (MQ=255)

                                             ttcttAAAACATTTGTAACATATTCTAGGTCATCCTCATAACGAATGACTTCACGAGGTACTTTCTCTTCTTTCCTAACAGGTGCAAAGCCAATCCCCATTGAATACGCTGCGGCACATCCAATGATAAAGCCACGCGCtt                                                                         <  2:321808/138‑1 (MQ=255)

                                                     aCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCt                                                                 >  1:354982/1‑141 (MQ=255)

                                                     aCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCATGCGCTTCAGGTCCt                                                                 >  2:383061/1‑141 (MQ=255)

                                                      cATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCACGTCCtc                                                                >  1:343927/1‑140 (MQ=255)

                                                       aTTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTAc                                                               <  1:165982/141‑1 (MQ=255)

                                                         ttGTACCATGTTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                             <  2:355746/141‑1 (MQ=255)

                                                           gTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAAGTCCTACAACg                                                           >  1:102692/1‑141 (MQ=255)

                                                              ccATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAACCTACAGGACAGCCAATGATAAAGCCACGCCCCTCAGGTCCTACCACGcta                                                        >  2:314545/1‑141 (MQ=255)

                                                                         gTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGTTCCTACAACGATATCAACATctct                                             >  2:25126/1‑141 (MQ=255)

                                                                          tCATACTCATAACGAGTGACTTCACGCGGTAATTTCCCTTCTTTTCTAACGGGTGCTAAGCCAATCCCCTTTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                            <  1:166933/141‑1 (MQ=255)

                                                                           cATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGt                                           >  1:408337/1‑141 (MQ=255)

                                                                                tCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACCATATCAACATCCCTGTCtttt                                      >  2:337259/1‑141 (MQ=255)

                                                                                 cATAACGAATGACTTCACGCGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCtgttt                                     >  1:417548/1‑140 (MQ=255)

                                                                                         aTGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACCGCCAATGATAAAGCCACGCGCTTCAAGTCCTACAACGATATCAACATCTCTGTCTTTTACGTATTCt                             >  2:55499/1‑141 (MQ=255)

                                                                                         aTGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCt                             <  1:21604/141‑1 (MQ=255)

                                                                                         aTGACTTCACGAGGTAATTTCCCTTCTATTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCt                             >  1:229502/1‑141 (MQ=255)

                                                                                          tGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCCTTTGCGTATTCTa                            >  1:74056/1‑141 (MQ=255)

                                                                                            aCTTCACGAGGTGATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACa                          >  1:154813/1‑141 (MQ=255)

                                                                                              ttCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAAt                        <  1:381501/141‑1 (MQ=255)

                                                                                                     ggTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCt                 >  1:65142/1‑141 (MQ=255)

                                                                                                       tAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGt               <  2:126303/141‑1 (MQ=255)

                                                                                                       tAATCTACCTTGTTTTCTAACGAGTGCAATGGTAATCCCCTGTTATTAAGCTACAGGACAGCTAATTATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGt               <  2:6529/141‑1 (MQ=255)

                                                                                                                  cttTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACACTTTTATCTGTTGCATAGCCat    >  1:270569/1‑141 (MQ=255)

                                                                                                                    tttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTTCGTATTCTACAATTTTATAAGTTGCATTGCCttat  >  2:251963/1‑141 (MQ=255)

CTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATAT  >  USA300TCH1516_ALE/1744320‑1744576

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