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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,016,401	C→T	G178G (GGC→GGT)	fliH →	negative regulator of FliI ATPase activity

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,016,401	0	C	T	97.1%	125.0 / ‑4.0	35	G178G (GGC→GGT)	fliH	negative regulator of FliI ATPase activity
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (16/18); total (16/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.53e-01

AGGTCATCGGTCAGACGCCAACGGTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGGCAGCACCAGGAGTG  >  NC_000913/2016256‑2016548

aGGTCATCGGTCAGACGCCAACGGTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTAc                                                                                                                                                <  2:562325/151‑1 (MQ=255)

              aCGCCAACGGTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCAtg                                                                                                                                  <  1:459972/151‑1 (MQ=255)

                   aaCGGTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCAtggctgg                                                                                                                             <  2:219553/151‑1 (MQ=255)

                      ggTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGgcgc                                                                                                                          >  2:534509/1‑151 (MQ=255)

                      ggTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGgcgc                                                                                                                          <  2:502950/151‑1 (MQ=255)

                             aaCTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCggg                                                                                                                   <  1:166769/151‑1 (MQ=255)

                                tCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCg                                                                                                                >  1:442423/1‑151 (MQ=255)

                                 cGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCg                                                                                                                >  1:251211/1‑150 (MQ=255)

                                 cGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCg                                                                                                                <  1:573513/150‑1 (MQ=255)

                                    cACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATcc                                                                                                            >  1:125412/1‑151 (MQ=255)

                                    cACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATcc                                                                                                            >  1:641964/1‑151 (MQ=255)

                                     aCTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATccc                                                                                                           >  1:264288/1‑151 (MQ=255)

                                       tGATCAAACAGACCCAACAGTTGTTTCATCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACTAGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCa                                                                                                          <  1:632775/150‑1 (MQ=255)

                                         aTCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCAccc                                                                                                       <  1:277357/151‑1 (MQ=255)

                                         aTCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCAccc                                                                                                       >  2:380944/1‑151 (MQ=255)

                                                    ccAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTgg                                                                                             <  1:263146/150‑1 (MQ=255)

                                                      aaCAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGCTCCCACCCTCCATCCTggcgg                                                                                          <  1:163334/151‑1 (MQ=255)

                                                        cAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCt                                                                                        >  1:630317/1‑151 (MQ=255)

                                                        cAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTggcggc                                                                                         <  2:50119/150‑1 (MQ=255)

                                                           ttgttgCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGt                                                                                      >  2:184036/1‑150 (MQ=255)

                                                                   gcaAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTcc                                                                             >  2:524326/1‑151 (MQ=255)

                                                                   gcaAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTcc                                                                             <  2:596286/151‑1 (MQ=255)

                                                                      aGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTccgcc                                                                          <  2:260383/151‑1 (MQ=255)

                                                                                     aggTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGAtctc                                                           >  1:275022/2‑151 (MQ=255)

                                                                                          aaCCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGc                                                      >  1:455774/1‑151 (MQ=255)

                                                                                              acaGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAgt                                                  >  2:402875/1‑151 (MQ=255)

                                                                                                            aCCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGAtctc                                                           >  2:147607/1‑128 (MQ=255)

                                                                                                            aCCCGGATGATCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGAtctc                                                           <  1:147604/128‑1 (MQ=255)

                                                                                                                      tCTGCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAActc                          >  1:181534/1‑151 (MQ=255)

                                                                                                                         gCAACGTGTGGATGATATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAAc                            <  2:147698/146‑1 (MQ=255)

                                                                                                                                   gatgatATGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGgcag             <  1:190317/151‑1 (MQ=255)

                                                                                                                                         atGCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGGCAGCACCa        <  2:177579/150‑1 (MQ=255)

                                                                                                                                           gCTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGGCAGCACCAGGa     <  1:661784/151‑1 (MQ=255)

                                                                                                                                            cTCGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGGCAGCACCAgg      >  1:450069/1‑149 (MQ=255)

                                                                                                                                              cGGTGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGGCAGCACCAGGAgtg  <  1:560798/151‑1 (MQ=255)

AGGTCATCGGTCAGACGCCAACGGTGGATAACTCGGCACTGATCAAACAGATCCAACAGTTGTTGCAGCAAGAACCGTTATTCAGCGGTAAACCACAGCTGCGCGTGCACCCGGATGATCTGCAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCCTCCATCCTGGCGGCTGTAAAGTCTCCGCCGATGAAGGCGATCTCGACGCCAGTGTCGCCACTCGCTGGCAAGAACTCTGCCGTCTGGCAGCACCAGGAGTG  >  NC_000913/2016256‑2016548

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A