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
A12 F999 I0 R1	73	59.3	4372352	98.6%	4311139	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	.	93.4%	238.5 / 16.5	61	coding (928/1017 nt)	waaJ	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand): ref base T (4/0); new base . (30/27); total (34/27)
Fisher's exact test for biased strand distribution p-value = 1.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-03

CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801024‑3801117

cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:187664/1‑50 (MQ=255)

cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:4021164/49‑1 (MQ=255)

cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:4028737/49‑1 (MQ=255)

cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:4274662/49‑1 (MQ=255)

 tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             >  1:4051501/1‑50 (MQ=255)

   taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  1:3600992/50‑1 (MQ=255)

   taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             <  1:3618265/48‑1 (MQ=255)

   taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             <  1:2408690/48‑1 (MQ=255)

    aaTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           >  1:3470735/1‑49 (MQ=255)

     aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta                                         <  1:4024980/50‑2 (MQ=255)

     aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                          >  1:236825/1‑49 (MQ=255)

     aTTCCTGAGATATAATGATGGTGCACTAAAAGATGTTTATATCtttttt                                          <  1:3097200/49‑1 (MQ=255)

        ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                      >  1:1719089/1‑49 (MQ=255)

        ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                      >  1:1260347/1‑49 (MQ=255)

        ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                      >  1:131899/1‑49 (MQ=255)

        ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                      >  1:1363451/1‑49 (MQ=255)

         cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:2102765/1‑50 (MQ=255)

          tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:3953853/1‑49 (MQ=39)

            agaTGTAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   <  1:4116361/48‑1 (MQ=38)

            agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:1104756/49‑1 (MQ=39)

            agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:70263/49‑1 (MQ=39)

            agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:3818137/49‑1 (MQ=39)

            agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:2633844/49‑1 (MQ=39)

              atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata                               <  1:3160759/50‑1 (MQ=255)

              atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                >  1:3632907/1‑49 (MQ=39)

               tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  1:2445657/1‑50 (MQ=255)

                 taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             <  1:4313774/49‑1 (MQ=39)

                 taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             <  1:2922719/49‑1 (MQ=39)

                 taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             <  1:3950283/49‑1 (MQ=39)

                 taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            >  1:4370213/1‑50 (MQ=255)

                 taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            >  1:2279737/1‑50 (MQ=255)

                  aaTGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            >  1:562694/1‑49 (MQ=39)

                   atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:1487512/49‑1 (MQ=39)

                   atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa                          <  1:2332749/50‑1 (MQ=255)

                    tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                         >  1:3931917/1‑50 (MQ=255)

                    tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                         >  1:2538519/1‑50 (MQ=255)

                    tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                         >  1:4250036/1‑50 (MQ=255)

                      atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                       <  1:310289/50‑1 (MQ=255)

                      atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                       <  1:4168763/50‑1 (MQ=255)

                      atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        <  1:329861/49‑1 (MQ=39)

                       tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      >  1:3306938/1‑50 (MQ=255)

                       tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:838807/50‑1 (MQ=255)

                        gTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg                     >  1:348019/1‑50 (MQ=255)

                         ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg                     >  1:1405991/1‑49 (MQ=39)

                           gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:4294769/1‑50 (MQ=255)

                            cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 >  1:3479764/1‑50 (MQ=255)

                            cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 <  1:2513177/50‑1 (MQ=255)

                            cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 >  1:3701561/1‑50 (MQ=255)

                            cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  <  1:2144220/49‑1 (MQ=39)

                            cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  <  1:4122069/49‑1 (MQ=39)

                            cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  <  1:392119/49‑1 (MQ=39)

                             aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                >  1:4126170/1‑50 (MQ=255)

                             aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                <  1:1077855/50‑1 (MQ=255)

                              cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  1:2136560/50‑1 (MQ=255)

                               tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              >  1:3852549/1‑50 (MQ=255)

                               tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              >  1:3590043/1‑50 (MQ=255)

                                aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:3051449/1‑50 (MQ=255)

                                aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:2920599/1‑50 (MQ=255)

                                 aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             <  1:807258/49‑1 (MQ=39)

                                 aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             <  1:1568278/49‑1 (MQ=39)

                                 aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:1583376/1‑50 (MQ=255)

                                  aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg           <  1:897597/50‑1 (MQ=255)

                                  aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:2993766/1‑49 (MQ=39)

                                    gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgag         <  1:3162767/50‑1 (MQ=255)

                                      tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag       <  1:1490843/50‑1 (MQ=255)

                                       gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:2045812/1‑50 (MQ=255)

                                        tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:2375405/1‑49 (MQ=39)

                                        tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:1537648/1‑49 (MQ=39)

                                        tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:490234/1‑49 (MQ=39)

                                        tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:355221/1‑49 (MQ=39)

                                         ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:663459/1‑50 (MQ=255)

                                           atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt   <  1:3187775/49‑1 (MQ=39)

                                           atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:1143637/1‑50 (MQ=255)

CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801024‑3801117

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