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
A15 F999 I0 R1	92	59.4	4455785	96.3%	4290920	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	.	96.1%	218.7 / 4.5	51	coding (928/1017 nt)	waaJ	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand): ref base T (1/1); new base . (24/25); total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117

gCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               >  1:203171/1‑50 (MQ=255)

gCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               >  1:1488982/1‑50 (MQ=255)

 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:2337803/1‑50 (MQ=255)

 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:441480/1‑50 (MQ=255)

 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:4188335/1‑50 (MQ=255)

 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:3278416/49‑1 (MQ=255)

    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt                                            <  1:1864577/49‑1 (MQ=255)

    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             <  1:899037/48‑1 (MQ=255)

      aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta                                         <  1:4066163/50‑2 (MQ=255)

      aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                          >  1:3308861/1‑49 (MQ=255)

      aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                          >  1:1616181/1‑49 (MQ=255)

      aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                          >  1:1450228/1‑49 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:192832/50‑3 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:3592805/50‑3 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:3781442/50‑3 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta                                         >  1:1412553/1‑48 (MQ=255)

       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta                                         >  1:2845985/1‑48 (MQ=255)

        tCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                       >  1:262286/1‑50 (MQ=255)

         ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                       <  1:2461514/49‑1 (MQ=255)

          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    <  1:3626491/50‑1 (MQ=255)

          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    <  1:2533261/50‑1 (MQ=255)

          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:2769439/1‑50 (MQ=255)

          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:1159817/1‑50 (MQ=255)

           tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:1324815/1‑49 (MQ=39)

           tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:2011041/1‑49 (MQ=39)

           tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:2871027/1‑49 (MQ=39)

            gagaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   >  1:3016302/1‑49 (MQ=39)

             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:2860357/49‑1 (MQ=39)

             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:260617/49‑1 (MQ=39)

              gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                <  1:482529/50‑1 (MQ=255)

              gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                <  1:2497656/50‑1 (MQ=255)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:2316845/50‑1 (MQ=255)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:2281265/50‑1 (MQ=255)

                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:2758546/50‑1 (MQ=255)

                  taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             <  1:3094950/49‑1 (MQ=39)

                  taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            >  1:2447320/1‑50 (MQ=255)

                  taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            <  1:211654/50‑1 (MQ=255)

                   aaTGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            >  1:1175972/1‑49 (MQ=39)

                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:1087363/49‑1 (MQ=39)

                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:168/49‑1 (MQ=39)

                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:1172968/49‑1 (MQ=39)

                     tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                         >  1:2530505/1‑50 (MQ=255)

                      gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        >  1:2995236/1‑50 (MQ=255)

                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                       >  1:3221108/1‑50 (MQ=255)

                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                       <  1:2102090/50‑1 (MQ=255)

                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        <  1:1362600/49‑1 (MQ=39)

                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      >  1:2458310/1‑50 (MQ=255)

                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:3899466/50‑1 (MQ=255)

                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg                     <  1:4245244/49‑1 (MQ=39)

                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg                     <  1:3061260/49‑1 (MQ=39)

                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc                    <  1:2578733/50‑1 (MQ=255)

                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc                    <  1:3738160/50‑1 (MQ=255)

                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:3723085/1‑50 (MQ=255)

                             cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 >  1:781379/1‑50 (MQ=255)

                             cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 <  1:1283825/50‑1 (MQ=255)

                              aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                >  1:1172459/1‑50 (MQ=255)

                               cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  1:4140776/50‑1 (MQ=255)

                                tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              >  1:1651604/1‑50 (MQ=255)

                                tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              >  1:127512/1‑50 (MQ=255)

                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:1912593/1‑50 (MQ=255)

                                    aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:235156/1‑48 (MQ=39)

                                    aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga          <  1:3115718/50‑1 (MQ=255)

                                       tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag       >  1:3954738/1‑50 (MQ=255)

                                          ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:3479225/1‑50 (MQ=255)

                                           tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    <  1:1047311/49‑1 (MQ=39)

                                           tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt   >  1:1089099/1‑50 (MQ=255)

                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:2104791/1‑50 (MQ=255)

                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:2274627/1‑50 (MQ=255)

GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `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