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
A2 F17 I0 R2	278	43.2	2215644	94.6%	2095999	61.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	782,109	T→C	20.9%	Q167R (CAG→CGG)	hlyE ←	hemolysin E

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	782,109	0	T	C	20.9%	85.9 / 20.1	43	Q167R (CAG→CGG)	hlyE	hemolysin E
Reads supporting (aligned to +/- strand): ref base T (17/17); new base C (7/2); total (24/19)
Fisher's exact test for biased strand distribution p-value = 2.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACCGGCGACGACACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTCCCGGAA  >  minE/782044‑782177

gACCGGCGACGACACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGaaa                                                                 <  1:1218806/71‑1 (MQ=255)

          gacACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCttt                                                       >  1:899021/1‑71 (MQ=255)

              ccGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAAt                                                                <  1:1373472/58‑1 (MQ=255)

                ggCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAg                                                              >  1:436162/1‑58 (MQ=255)

                ggCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAg                                                              >  1:2031405/1‑58 (MQ=255)

                 gCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGa                                                                   <  1:2014015/52‑1 (MQ=255)

                     cGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGaaaa                                             <  1:185867/70‑1 (MQ=255)

                          ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGATAAATCAt                                        <  1:1235183/70‑1 (MQ=255)

                            ggCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTgg                                     >  1:1724692/1‑71 (MQ=255)

                                tatGCTTCCTTCCTGATTTTATCTAGCTGTGACTGGAAATAg                                                              <  1:1237159/42‑1 (MQ=255)

                                tatGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCtttt                                                      <  1:573791/50‑1 (MQ=255)

                                tatGCTTCCTTCCTGATTTTATATACCTTTGACTGGAAATAg                                                              <  1:412106/42‑1 (MQ=38)

                                  tGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAg                                                              >  1:971020/1‑40 (MQ=255)

                                  tGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCtttttt                                                    >  1:1301672/1‑50 (MQ=255)

                                  tGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCtttttt                                                    >  1:235496/1‑50 (MQ=255)

                                  tGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACt                               >  1:1706366/1‑71 (MQ=255)

                                  tGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACt                               >  1:1632692/1‑71 (MQ=255)

                                  tGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACt                               >  1:1208362/1‑71 (MQ=255)

                                   gCTTCCTTCCTGATTTTATCTACCTGTGACTCGAAATAGCTGCTTTTTTCTGAAAAATCATTg                                      <  1:1759837/63‑1 (MQ=255)

                                   gCTTACTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                                      >  1:580314/1‑47 (MQ=255)

                                    cttccttcCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTgg                             >  1:1692651/1‑71 (MQ=255)

                                       ccttcctGATTTTATCTACCTGTGACTGGAAATAgct                                                            >  1:1780001/1‑37 (MQ=255)

                                       ccttcctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGc                            <  1:265904/69‑1 (MQ=255)

                                        cttcctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATc                                          <  1:91263/54‑1 (MQ=255)

                                        cttcctGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTc                                                   >  1:693682/1‑45 (MQ=255)

                                         ttcctGATTTTATCTACCTGTGACTGGAAATAGCTGCttttt                                                     <  1:1010248/42‑1 (MQ=255)

                                         ttcctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATc                                          <  1:983823/53‑1 (MQ=255)

                                          tcctGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTATGAAAAAt                                           <  1:1045159/51‑1 (MQ=255)

                                               aTTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:239850/1‑57 (MQ=255)

                                               aTTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:219346/1‑57 (MQ=255)

                                               aTTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:1996030/1‑57 (MQ=255)

                                                ttttATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:462979/1‑56 (MQ=255)

                                                ttttATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:530814/1‑56 (MQ=255)

                                                ttttATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:1104316/1‑56 (MQ=255)

                                                ttttATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCt                           <  1:907252/61‑1 (MQ=255)

                                                   tATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCcag               <  1:1075416/70‑1 (MQ=255)

                                                         ccTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTc        <  1:660094/71‑1 (MQ=255)

                                                         ccTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATTTAACGCCAGCAGTTTc        <  1:1940581/71‑1 (MQ=255)

                                                           tgtgACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAAc                                >  1:989964/1‑45 (MQ=255)

                                                           tgtgACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTccc      >  1:932341/1‑71 (MQ=255)

                                                            gtgACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTCCCg     >  1:1148019/1‑71 (MQ=255)

                                                            gtgACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTCCCg     >  1:1032400/1‑71 (MQ=255)

                                                               aCTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTCCCGGaa  <  1:81032/71‑1 (MQ=255)

                                                                 tGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTa                                  <  1:657682/37‑1 (MQ=255)

                                                                 tGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTa                                  <  1:1598862/37‑1 (MQ=255)

GACCGGCGACGACACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAACGCCAGCAGTTTCCCGGAA  >  minE/782044‑782177

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