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 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,079,114	T→C	69.0%	H201R (CAC→CGC)	natA_1 ←	ABC transporter ATP‑binding protein NatA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,079,114	0	T	C	69.0%	38.1 / 20.9	32	H201R (CAC→CGC)	natA_1	ABC transporter ATP‑binding protein NatA
Reads supporting (aligned to +/- strand): ref base T (6/4); new base C (16/6); total (22/10)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01

GTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAG  >  USA300TCH1516_ALE/2078979‑2079249

gTACGCTTATGTTGTTCATAAATATGGAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATg                                                                                                                                    >  2:191627/1‑141 (MQ=255)

                    aataaGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTc                                                                                                                >  2:279865/1‑141 (MQ=255)

                      taaGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTa                                                                                                              >  2:4815/1‑141 (MQ=255)

                        aGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTaaa                                                                                                            >  1:219229/1‑141 (MQ=255)

                          tAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACATTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCGAAATc                                                                                                          >  1:82831/1‑141 (MQ=255)

                          tAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATc                                                                                                          >  1:324135/1‑141 (MQ=255)

                           agagATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCt                                                                                                         >  1:257563/1‑141 (MQ=255)

                            gagaTGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTg                                                                                                        <  2:51208/141‑1 (MQ=255)

                             agaTGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTga                                                                                                       <  2:282187/141‑1 (MQ=255)

                                  cTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATaa                                                                                                  >  2:30007/1‑141 (MQ=255)

                                     aTTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCCCCGTCACTTAAGCGCATGATATCATCAGCTATTTTTTCTAAATCTGAGATAAtgt                                                                                               >  1:52200/1‑141 (MQ=255)

                                     aTTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGACATacatt                                                                                               >  2:275672/1‑137 (MQ=255)

                                       tcatcatcaAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAAtgtgt                                                                                             >  1:245294/1‑141 (MQ=255)

                                               aaGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACAt                                                                                     <  1:56494/141‑1 (MQ=255)

                                                    ccTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAata                                                                                >  1:258375/1‑141 (MQ=255)

                                                        aaTAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGt                                                                            <  1:385662/141‑1 (MQ=255)

                                                              accacTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATATGACATAATGTGTGTCGACATGAATATTGTTTTAtt                                                                      >  2:191489/1‑141 (MQ=255)

                                                                      caACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATGATGTGTGTCGACATGCATATTGTTTTATTTTCATaaa                                                              >  2:16154/1‑141 (MQ=255)

                                                                      caACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGACTATTGTTTTATTTTCATCaa                                                              <  1:239238/141‑1 (MQ=255)

                                                                                tCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTg                                                    >  1:136181/1‑141 (MQ=255)

                                                                                tCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGGCGACATGAATATTGTTTTATTTTCATAAATTAATTATTg                                                    >  2:179825/1‑141 (MQ=255)

                                                                                  tttGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCt                                                  <  2:308343/141‑1 (MQ=255)

                                                                                    tGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGa                                                >  1:178723/1‑141 (MQ=255)

                                                                                        aCAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTTTTTGTTTTTGATAATGTGTGTCGACATGATTATTGTTTTTTTTTATTGGATTTATTCTTGTTGTAttt                                            >  2:286035/1‑140 (MQ=255)

                                                                                                        aCCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCAtt                            >  1:266314/1‑141 (MQ=255)

                                                                                                            tttAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTTTTTCTCTGATAATGTTTGTCGACATGTATATTGTTTTATTTTCGTCACTTAATTATTGTTGAGTTTTTGCCATTAGTTCATTTCtt                        >  2:206316/1‑140 (MQ=255)

                                                                                                                 taTAATTTCACCGTTACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTaa                   <  2:193949/140‑1 (MQ=255)

                                                                                                                   tAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAgg                 <  2:393101/141‑1 (MQ=255)

                                                                                                                     aCTTCACCGTAACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGa               <  1:223029/141‑1 (MQ=255)

                                                                                                                            cGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGAc        >  2:66543/1‑141 (MQ=255)

                                                                                                                                aCTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGa    >  1:27100/1‑141 (MQ=255)

                                                                                                                                  ttAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAg  <  1:72392/141‑1 (MQ=255)

GTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAG  >  USA300TCH1516_ALE/2078979‑2079249

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