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
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,378,355	T→C	53.3%	K188E (AAA→GAA)	yjeJ ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,378,355	0	T	C	53.3%	13.7 / 81.7	60	K188E (AAA→GAA)	yjeJ	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (23/5); new base C (19/13); total (42/18)
Fisher's exact test for biased strand distribution p-value = 8.93e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01

GCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAACGTCGTATAAC  >  W3110S.gb/4378296‑4378422

gCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCgg                                                            >  1:527707/1‑69 (MQ=255)

    cTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTg                                                         >  1:1786368/1‑68 (MQ=255)

    cTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTg                                                         >  1:3493290/1‑68 (MQ=255)

     tttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                                       <  1:423516/69‑1 (MQ=255)

     tttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:3662647/69‑1 (MQ=255)

      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                                       <  1:182973/68‑1 (MQ=255)

      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                                       >  1:1557719/1‑68 (MQ=255)

      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                                       <  1:1014416/68‑1 (MQ=255)

      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                                       >  1:3574481/1‑68 (MQ=255)

      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       >  1:1117820/1‑68 (MQ=255)

       tCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTc                                                                    >  1:141515/1‑54 (MQ=255)

       tCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       >  1:2042623/1‑67 (MQ=255)

         aTCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGaa                                                     <  1:770824/67‑1 (MQ=255)

            tttAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTg                                                         >  1:1651847/1‑60 (MQ=255)

              tAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:972605/60‑1 (MQ=255)

              tAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:2694384/60‑1 (MQ=255)

              tAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:1527312/60‑1 (MQ=255)

              tAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:1537166/60‑1 (MQ=255)

                 aGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:1078447/57‑1 (MQ=255)

                 aGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTggg                                                       <  1:547014/57‑1 (MQ=255)

                 aGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCa                                            <  1:3180558/68‑1 (MQ=255)

                  gCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCa                                            <  1:1225228/67‑1 (MQ=255)

                       aaaGCACCGCCAGATAATGGTCGAACAAGTTATGTTTcc                                                                   <  1:1089694/39‑1 (MQ=255)

                        aaGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                                     >  1:3564348/1‑68 (MQ=255)

                        aaGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                                     >  1:2515103/1‑68 (MQ=255)

                        aaGCACAGACAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGaa                                                     >  1:476854/1‑52 (MQ=255)

                             ccGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGgtgt                                              >  1:1350503/1‑54 (MQ=255)

                             acGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGgtgt                                              >  1:2716863/2‑54 (MQ=255)

                              cGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGcc                              <  1:1539106/69‑1 (MQ=255)

                              cGCCAGATAATGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGcc                              <  1:3419560/69‑1 (MQ=255)

                                     tAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGaa                                                     >  1:1075419/1‑39 (MQ=255)

                                     tAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGaa                                                     >  1:186027/1‑39 (MQ=255)

                                     tAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGaa                                                     >  1:1523478/1‑39 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAg                                                  >  1:863784/1‑41 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAg                                                  >  1:3385371/1‑41 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCata                                          <  1:2794866/49‑1 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGc                               >  1:3419051/1‑60 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCt                      >  1:1343221/1‑69 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGta                        >  1:1376358/1‑66 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTc                        >  1:637084/1‑67 (MQ=255)

                                      aaTGGTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCt                      >  1:3450242/1‑69 (MQ=255)

                                       aTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGa                                   >  1:123900/1‑55 (MQ=255)

                                       aTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCt                      >  1:128170/1‑68 (MQ=255)

                                          gTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATa                                                   >  1:1583060/1‑36 (MQ=255)

                                          gTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATa                                                   >  1:1102763/1‑36 (MQ=255)

                                          gTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATa                                                   >  1:1672747/1‑36 (MQ=255)

                                          gTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTcc                                      >  1:1205876/1‑49 (MQ=255)

                                          gTCGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTcc                                      <  1:1365769/49‑1 (MQ=255)

                                            cGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAg                 >  1:3282000/1‑68 (MQ=255)

                                            cGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAg                 >  1:3554580/1‑68 (MQ=255)

                                            cGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAg                                    >  1:2794740/1‑49 (MQ=255)

                                            cGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAg                                    >  1:2997069/1‑49 (MQ=255)

                                            cGAACAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAg                                    >  1:1833713/1‑49 (MQ=255)

                                                cAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAAc            >  1:1683587/1‑69 (MQ=255)

                                                cAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCaa             >  1:1446432/1‑68 (MQ=255)

                                                cAAGTTATGTTCCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAAc            >  1:590283/1‑69 (MQ=255)

                                                     tATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAAcgtcg        >  1:990224/1‑68 (MQ=255)

                                                     tATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAAcgtcg        >  1:975027/1‑68 (MQ=255)

                                                     tATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAAcgtcg        >  1:1913769/1‑68 (MQ=255)

                                                     tATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAAcgtcg        >  1:1846926/1‑68 (MQ=255)

                                                         tttCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAACGTCGtata    <  1:1513488/68‑1 (MQ=255)

                                                           tCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAACGTCGTATAAc  >  1:2681614/1‑68 (MQ=255)

                                                           tCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAACGTCGTATAAc  >  1:968431/1‑68 (MQ=255)

GCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCAGTCAACGTCGTATAAC  >  W3110S.gb/4378296‑4378422

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A