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
A5 F58 I0 R1	46	56.2	1222162	96.0%	1173275	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	973,213	C→A	100%	E175* (GAG→TAG)	yitU_1 ←	5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	973,213	0	C	A	90.2%	104.9 / 4.1	41	E175* (GAG→TAG)	yitU_1	5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU
Reads supporting (aligned to +/- strand): ref base C (1/3); new base A (20/17); total (21/20)
Fisher's exact test for biased strand distribution p-value = 3.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTA  >  USA300TCH1516_ALE/973077‑973346

tCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAata                                                                                                                                   >  1:547503/1‑141 (MQ=255)

         ccGAATGCATTAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                          <  2:203458/141‑1 (MQ=255)

         ccGAATGACATAATATTATTTCGGTCACTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                          <  2:343969/141‑1 (MQ=255)

          cGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAGTGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCAt                                                                                                                         >  1:410051/1‑141 (MQ=255)

           gAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATa                                                                                                                        <  1:378636/141‑1 (MQ=255)

              tGCAATAATATCATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATaaaa                                                                                                                     <  1:303870/141‑1 (MQ=255)

               gCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaaaaa                                                                                                                    <  2:518393/141‑1 (MQ=255)

                                   aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAGATGAGTAAGCATATTTTTGAt                                                                                                >  1:236386/1‑141 (MQ=255)

                                     tatTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAttt                                                                                              <  1:424839/141‑1 (MQ=255)

                                         tAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAgg                                                                                          >  1:396900/1‑141 (MQ=255)

                                         tAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAgg                                                                                          >  2:195928/1‑141 (MQ=255)

                                                    tAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACttt                                                                               >  2:42757/1‑141 (MQ=255)

                                                     aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttc                                                                              <  1:466717/141‑1 (MQ=255)

                                                         tGCTCCATGCCTCTTGCGTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCg                                                                          <  1:166456/141‑1 (MQ=255)

                                                          gCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCgg                                                                         >  1:577413/1‑141 (MQ=255)

                                                               aTGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCa                                                                    >  2:505950/1‑141 (MQ=255)

                                                                      ttGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGCAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTaaaa                                                             <  2:448605/141‑1 (MQ=255)

                                                                              ttaATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGACGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTa                                                     <  2:417504/141‑1 (MQ=255)

                                                                                   aCCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTCTTTTACTTTCTTAGCCTTCAATTAAAATTGTGGTAGGTGa                                                >  2:581285/1‑141 (MQ=255)

                                                                                    ccAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGAt                                               >  1:252116/1‑141 (MQ=255)

                                                                                     cAAGTTTTACAATTTCAATGACAGGTAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGAtt                                              <  2:396900/141‑1 (MQ=255)

                                                                                     cAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGAtt                                              <  1:195928/141‑1 (MQ=255)

                                                                                       aGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCGATTAAAATTGATGTAGGGGATTCt                                            >  1:571892/1‑141 (MQ=255)

                                                                                            tACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCaa                                       >  1:171073/1‑141 (MQ=255)

                                                                                             aCAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAg                                      >  2:40925/1‑141 (MQ=255)

                                                                                               aacttCAATGACAGGGAATGGTGCGCCCCAGCTGCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTg                                    <  2:47378/138‑1 (MQ=255)

                                                                                                 tttCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGa                                  <  1:521413/141‑1 (MQ=255)

                                                                                                 ttcaaaTGACAGGGGATGGTGCGCCCCAGCGTGGGTGGTAAATATGACCGGCATAAAAATGAGTAAGCATATTTTTGACTTCAGGTGTTTTACTTTCTTCGGCTTCAATTAAAATGGAGGTAGGGGATTCTTTCAAGTGGa                                  <  2:22806/137‑1 (MQ=255)

                                                                                                   tCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCTAGTGGACa                                <  2:527164/141‑1 (MQ=255)

                                                                                                      aTGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGt                             >  1:336920/1‑141 (MQ=255)

                                                                                                        gACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTCAGGTAGGGGATTCTTTCCAGTGGCCCAGTaa                           >  1:285005/1‑141 (MQ=255)

                                                                                                           aGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAAtt                        >  2:78315/1‑141 (MQ=255)

                                                                                                           aGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAAtt                        >  2:590963/1‑141 (MQ=255)

                                                                                                              gAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTAcc                     >  1:183521/1‑141 (MQ=255)

                                                                                                                 tGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGt                  >  2:293607/1‑141 (MQ=255)

                                                                                                                 tGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGt                  >  1:423665/1‑141 (MQ=255)

                                                                                                                 tGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCAGATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCACTTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACAAgg                  >  2:372199/1‑140 (MQ=255)

                                                                                                                  ggTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGtt                 <  2:411355/141‑1 (MQ=255)

                                                                                                                              cGTCGATGCTAAATATGGTCGTCATAAAAATGAGTAAGAGTATTGTGGGTTTCGGGTGGTTTTCTTTCTTAGGCTTCAATTAAAATTGAGGTGGGTGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGa     <  2:83400/141‑1 (MQ=255)

                                                                                                                              cGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGa     <  2:236386/141‑1 (MQ=255)

                                                                                                                                 cGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTa  <  1:185782/141‑1 (MQ=255)

TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTA  >  USA300TCH1516_ALE/973077‑973346

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