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
A21 F999 I0 R1	108	30.5	2257647	98.2%	2217009	49.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,801,078	(T)_7→6	coding (922/1017 nt)	waaJ ←	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,801,072	0	T	.	92.6%	101.1 / 5.1	27	coding (928/1017 nt)	waaJ	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/2); new base . (10/15); total (10/17)
Fisher's exact test for biased strand distribution p-value = 5.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117

gCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               >  1:1351248/1‑50 (MQ=255)

 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:419995/1‑50 (MQ=255)

    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  1:744639/50‑1 (MQ=255)

    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  1:2235398/50‑1 (MQ=255)

    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           >  1:1572652/1‑50 (MQ=255)

    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt                                            <  1:184554/49‑1 (MQ=255)

     aaTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           >  1:1061980/1‑49 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:896583/50‑3 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:1018638/50‑3 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:1459703/50‑3 (MQ=255)

         ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                       <  1:126485/49‑1 (MQ=255)

          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaatc                                     <  1:854913/50‑3 (MQ=255)

          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    <  1:1440470/50‑1 (MQ=255)

             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:267493/49‑1 (MQ=39)

             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:1925903/49‑1 (MQ=39)

              gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                <  1:1607504/50‑1 (MQ=255)

               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                >  1:868488/1‑49 (MQ=39)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  1:2191326/1‑50 (MQ=255)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  1:1424153/1‑50 (MQ=255)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:2194021/50‑1 (MQ=255)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:1604995/50‑1 (MQ=255)

                 ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             >  1:672076/1‑50 (MQ=255)

                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:1567539/49‑1 (MQ=39)

                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        <  1:1970210/49‑1 (MQ=39)

                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:1543052/50‑1 (MQ=255)

                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc                    <  1:761471/50‑1 (MQ=255)

                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:1736796/1‑50 (MQ=255)

                               cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  1:76465/50‑1 (MQ=255)

                                 aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:1398768/1‑50 (MQ=255)

                                 aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:2099277/1‑50 (MQ=255)

                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            <  1:1610528/50‑1 (MQ=255)

                                   aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg           <  1:668223/50‑1 (MQ=255)

                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga        <  1:2127225/50‑1 (MQ=255)

                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga          >  1:39009/1‑48 (MQ=39)

                                          ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:1941392/1‑50 (MQ=255)

                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt   <  1:1828491/49‑1 (MQ=39)

                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:1427247/1‑50 (MQ=255)

GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A