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
A73 F1 I1 R1	21	62.0	3993596	96.1%	3837845	76.0

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	1,601,233	T→C	intergenic (+162/‑154)	ydfK → / → pinQ	predicted DNA‑binding transcriptional regulator/predicted site‑specific recombinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	1,601,233	0	T	C	90.6%	61.3 / 1.3	32	intergenic (+162/‑154)	ydfK/pinQ	predicted DNA‑binding transcriptional regulator/predicted site‑specific recombinase
Reads supporting (aligned to +/- strand): ref base T (0/3); new base C (19/10); total (19/13)
Fisher's exact test for biased strand distribution p-value = 5.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

AATAACACGCAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTT  >  REL606/1601159‑1601272

aaTAACACGCAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTc                                        <  2:1732542/76‑1 (MQ=34)

        gCAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATc                                >  1:1220238/1‑76 (MQ=21)

         cAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCg                               <  1:1431075/76‑1 (MQ=34)

         cAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCg                               <  1:584945/76‑1 (MQ=21)

         cAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCg                               <  1:1825567/76‑1 (MQ=21)

           acacTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGAt                             <  1:1763504/76‑1 (MQ=21)

           acacTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGAt                             <  1:131000/76‑1 (MQ=21)

           acacTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGAt                             <  1:1282449/76‑1 (MQ=21)

            cacTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGAtt                            >  1:1242122/1‑76 (MQ=21)

                aTTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTgg                        >  1:930676/1‑76 (MQ=21)

                  tcttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGt                      >  2:16778/1‑76 (MQ=21)

                  tcttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGt                      >  2:1473079/1‑76 (MQ=21)

                   cttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGtc                     >  1:1387368/1‑76 (MQ=21)

                   cttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGtc                     >  1:1387361/1‑76 (MQ=21)

                    ttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGtct                    >  1:1564523/1‑76 (MQ=21)

                    ttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGtct                    >  1:1015696/1‑76 (MQ=21)

                    ttcttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGtct                    <  2:1553610/76‑1 (MQ=21)

                      cttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCa                  >  2:201408/1‑76 (MQ=21)

                       ttcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCAc                 >  2:500252/1‑76 (MQ=21)

                        tcCTTGAGTCCGCCTGGAGCTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGGCTCAcc                >  1:483240/1‑76 (MQ=11)

                        tcCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCAcc                >  1:730971/1‑76 (MQ=21)

                         ccTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCa               >  1:333272/1‑76 (MQ=21)

                          cTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCaa              >  2:1547464/1‑76 (MQ=21)

                          cTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCaa              <  2:714861/76‑1 (MQ=21)

                           ttGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCaaa             <  2:1226809/76‑1 (MQ=21)

                             gAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCAAAAt           >  2:1083150/1‑76 (MQ=21)

                              aGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCAAAAtt          <  1:1442698/76‑1 (MQ=21)

                                tCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCAAAATTAc        <  1:269119/76‑1 (MQ=21)

                                 ccGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCAAAATTACg       >  2:48272/1‑76 (MQ=21)

                                     cTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGt   >  2:1654014/1‑76 (MQ=17)

                                      tGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGtt  <  2:868081/76‑1 (MQ=31)

                                      tGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTCCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGtt  >  2:1776132/1‑76 (MQ=14)

AATAACACGCAACACTATTCTTCTTCCTTGAGTCCGCCTGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTT  >  REL606/1601159‑1601272

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

N/A