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 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,011,516	C→T	A19V (GCC→GTC)	yqeA →	putative amino acid kinase YqeA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,011,516	0	C	T	98.1%	174.5 / ‑4.4	52	A19V (GCC→GTC)	yqeA	putative amino acid kinase YqeA
Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (29/22); total (30/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

AACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTGGGCATGATTAACCAGGCCTTTGAAGC  >  NC_000913/3011388‑3011642

aaCCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGa                                                                                                                      <  2:127828/140‑1 (MQ=255)

             tcccGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTa                                                                                                              >  1:101544/1‑135 (MQ=255)

             tcccGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTa                                                                                                              <  2:101544/135‑1 (MQ=255)

               cagTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTa                                                                                                      >  1:162207/3‑140 (MQ=255)

                   gCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTtc                                                                                                  >  2:695909/1‑140 (MQ=255)

                         aCCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGc                                                                                            >  2:13286/1‑140 (MQ=255)

                              tGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAAttg                                                                                       >  2:241269/1‑140 (MQ=255)

                                       tCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTaa                                                                              <  1:241269/140‑1 (MQ=255)

                                       tCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTaa                                                                              <  1:854658/140‑1 (MQ=255)

                                        cTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAAt                                                                             >  1:413403/1‑140 (MQ=255)

                                              acaATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCa                                                                       <  1:13286/140‑1 (MQ=255)

                                                aaTCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCa                                                                       <  2:350191/138‑1 (MQ=255)

                                                aaTCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCa                                                                       >  1:350191/1‑138 (MQ=255)

                                                aaTCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAgg                                                                     >  2:581120/1‑140 (MQ=255)

                                                aaTCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAgg                                                                     <  2:162207/140‑1 (MQ=255)

                                                aaTCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAgg                                                                     >  1:363505/1‑140 (MQ=255)

                                                aaTCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAgg                                                                     <  2:363505/140‑1 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  1:77780/1‑140 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  1:86533/1‑140 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  2:765504/1‑140 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  1:636950/1‑140 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  2:488781/1‑140 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  2:891962/1‑140 (MQ=255)

                                                  tCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAAATGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa                                                                   >  2:120081/1‑140 (MQ=255)

                                                     aGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAATTTACTCCTAAGGCTATTGTGGTTTTAATTGCCCAGGGCCa                                                                 >  1:529033/1‑140 (MQ=255)

                                                     aGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACAt                                                                >  1:656350/1‑140 (MQ=255)

                                                     aGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACAt                                                                >  1:222611/1‑140 (MQ=255)

                                                     aGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACAt                                                                >  1:540058/1‑140 (MQ=255)

                                                         tgatgaGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAg                                                            <  1:695909/140‑1 (MQ=255)

                                                            tgagtgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTa                                                         >  1:635044/1‑140 (MQ=255)

                                                            tgagtgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTa                                                         >  1:323480/1‑140 (MQ=255)

                                                            tgagtgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTa                                                         >  1:448844/1‑140 (MQ=255)

                                                              agtgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATc                                                       >  1:468327/1‑140 (MQ=255)

                                                               aggaagAAAAAAGGGTAACGAAATTGGTCCTGGCCTTGGCCGGAACTGGCCGGGGCGAGGCCTTGGTGGGGCAAATGAAGCCGGAAAAAA‑TTACTTCTCAGGCTATTGTTGATTTAATTGCCCAGGGACATGAAGTTATc                                                       <  2:529033/135‑1 (MQ=255)

                                                                tgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt                                                     <  1:891962/140‑1 (MQ=255)

                                                                tgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt                                                     >  2:387306/1‑140 (MQ=255)

                                                                tgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt                                                     <  2:77780/140‑1 (MQ=255)

                                                                tgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt                                                     <  2:598562/140‑1 (MQ=255)

                                                                tgagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt                                                     <  2:656350/140‑1 (MQ=255)

                                                                 gagGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTc                                                    >  2:338949/1‑140 (MQ=255)

                                                                          tGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGt                                           >  2:516970/1‑140 (MQ=255)

                                                                            aGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTaa                                         <  2:413403/140‑1 (MQ=255)

                                                                              tAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACg                                       <  2:540058/140‑1 (MQ=255)

                                                                              tAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGCAACg                                       <  2:222611/140‑1 (MQ=255)

                                                                                        tGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAgg                              <  2:636950/140‑1 (MQ=255)

                                                                                         gTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGt                             <  2:431981/140‑1 (MQ=255)

                                                                                            ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTggg                          <  1:488781/140‑1 (MQ=255)

                                                                                            ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTggg                          <  2:635044/140‑1 (MQ=255)

                                                                                            ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTggg                          >  1:642357/1‑140 (MQ=255)

                                                                                            ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTggg                          <  1:588486/140‑1 (MQ=255)

                                                                                                    gggCGGGAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTGGGCATGATTa                  >  1:412035/1‑140 (MQ=255)

                                                                                                        gggAATGCGCTGGGCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTGGGCATGATTAACCa              <  1:516970/140‑1 (MQ=255)

                                                                                                                    ggCGATGACCTGGTCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTGGGCATGATTAACCAGGCCTTTGAAGc  >  2:97597/1‑140 (MQ=255)

AACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAA‑GAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAA‑TTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGTCACTCATGGTAACGGGCCGCAGGTGGGCATGATTAACCAGGCCTTTGAAGC  >  NC_000913/3011388‑3011642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A