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
A19 F74 I0 R1	21	36.7	824702	95.0%	783466	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,292	A→T	100%	I127N (ATT→AAT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,292	0	A	T	91.2%	80.7 / ‑0.5	31	I127N (ATT→AAT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base A (2/1); new base T (9/19); total (11/20)
Fisher's exact test for biased strand distribution p-value = 2.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATTCGTCGTATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTA  >  USA300TCH1516_ALE/1744154‑1744424

tattCGTCGTATGAGATTAAACTCATAACATCGTAATCTTTACTTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTACTGCTTCATTc                                                                                                                                    >  2:401765/1‑141 (MQ=255)

 attCGTCGTATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCg                                                                                                                                   <  1:42090/141‑1 (MQ=255)

   tcgtcgTATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTa                                                                                                                                 <  1:213923/141‑1 (MQ=255)

     gtcgtATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATGAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTacc                                                                                                                               <  2:358463/141‑1 (MQ=255)

      gcgtATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTacca                                                                                                                              <  1:45787/140‑1 (MQ=255)

        gtATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTaccacc                                                                                                                            <  2:180160/141‑1 (MQ=255)

               aTTAAACTCATAACCGAGTAATTTTGAAGTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCt                                                                                                                     >  2:360361/1‑141 (MQ=255)

                 tAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCtaa                                                                                                                   <  1:36675/141‑1 (MQ=255)

                    aCTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAGTTTTATTGCTGCTTCATTCGTACCACCAGTAGCtaataa                                                                                                                <  1:400802/141‑1 (MQ=255)

                                          aTTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATCACGCCTAATTTTTCAACTAATTTTATTAATGACTCAATCGTACCACCATCAGCTAATAAATCATCTGTAATTATCACCCgc                                                                                          >  2:247449/1‑140 (MQ=255)

                                               ttCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGAcc                                                                                     >  1:85753/1‑141 (MQ=255)

                                                             aaTATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGTCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCAt                                                                       <  2:365475/141‑1 (MQ=255)

                                                             aaTATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACTACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCAt                                                                       <  1:88621/141‑1 (MQ=255)

                                                              atatTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATc                                                                      <  2:355096/141‑1 (MQ=255)

                                                               tatTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCt                                                                     >  1:35498/1‑141 (MQ=255)

                                                               tatTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTCCATCt                                                                     >  2:242517/1‑141 (MQ=255)

                                                                  ttcaattcaaTTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTtg                                                                  >  1:203599/1‑141 (MQ=255)

                                                                       ttcaattATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGcct                                                             <  2:404677/141‑3 (MQ=255)

                                                                             tataAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTaa                                                       <  1:379848/141‑1 (MQ=255)

                                                                                 aaTGCAATACCTACTACGTTACCGACTTATTTTTCAATTAATTTTATTGCTGTTTAATTCGTACCACCAGTAGGGAATAAATCATCTGTAATTAACACATGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACa                                                   <  2:186594/141‑1 (MQ=255)

                                                                                         aCCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTATTTAACACACGTTGACCTGGTTTAATTTCATCTTTTTGTATTTTTAAAACATTTTTaac                                           >  1:91186/1‑139 (MQ=255)

                                                                                           ctactaCGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCCCCCGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGCTAAAACCtttttcccgt                                         >  1:308457/1‑134 (MQ=255)

                                                                                            tactacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCata                                        <  2:35498/141‑1 (MQ=255)

                                                                                               tacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTc                                     <  1:287646/141‑1 (MQ=255)

                                                                                                      ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCa                              <  1:247449/141‑1 (MQ=255)

                                                                                                               ttttCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGtcataatcataa                     >  2:54966/1‑141 (MQ=255)

                                                                                                                  tCAACTAATTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGa                  >  2:93299/1‑141 (MQ=255)

                                                                                                                   cAACCAATTTTAGTGCTGCGTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                 <  1:161471/141‑1 (MQ=255)

                                                                                                                         aTTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGTCCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACtt           <  1:98366/141‑1 (MQ=255)

                                                                                                                         aTTTTATTGCTGCTTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACtt           <  1:121689/141‑1 (MQ=255)

                                                                                                                                  ctgctTCATTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTa  <  2:405958/141‑1 (MQ=255)

TATTCGTCGTATGAGATTAAACTCATAACATCGTAATCTTTAATTTTTTCAATACCATTTAAATATTTCAATTCAATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTA  >  USA300TCH1516_ALE/1744154‑1744424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A