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
A25 F111 I0 R1	33	34.4	1317450	90.1%	1187022	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,196,253	G→A	54.7%	intergenic (‑154/+79)	thiC ← / ← rsd	phosphomethylpyrimidine synthase/regulator of sigma D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,196,253	0	G	A	54.7%	1.9 / 45.7	42	intergenic (‑154/+79)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand): ref base G (8/10); new base A (11/11); total (19/23)
Fisher's exact test for biased strand distribution p-value = 7.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.64e-01

TTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAATCAGCTTATC  >  NC_000913/4196116‑4196385

ttAAGGACGTGGCTGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGt                                                                                                                                 <  1:650564/143‑1 (MQ=255)

    ggACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAg                                                                                                                             <  2:129147/143‑1 (MQ=255)

     gACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCCCCGGCATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAga                                                                                                                            >  1:374050/1‑142 (MQ=255)

     gACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTCCGCAGGTATTAGCCTGATCAGGTTCCGCGTATCCCGAATAAACGGTCTCAACCAGTTAAgg                                                                                                                            >  2:276274/1‑143 (MQ=255)

                tCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACaa                                                                                                                 >  1:594148/1‑143 (MQ=255)

                  aGACGACGTATGATGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGa                                                                                                               <  2:23265/143‑1 (MQ=255)

                         ggATGAGGCACGCGACGATCGCCGCAGGGGCGATGCGATAGCAGATTCACTCTTTTTCCATTCGTCGGTCGTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGc                                                                                                        <  1:336344/143‑1 (MQ=255)

                         ggATGAAGCAAGAGACGATCGCCGCAGGTGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGc                                                                                                        <  1:55347/143‑1 (MQ=255)

                                   agagACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATg                                                                                              >  1:388765/1‑143 (MQ=255)

                                     agaCGAGCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATggg                                                                                            <  2:150270/143‑1 (MQ=255)

                                        cGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCa                                                                                         >  1:536014/1‑143 (MQ=255)

                                         gATCGCCGCAGGGGCGATGCGATAGCAGATCAACGCTTGGTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGAGCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAt                                                                                        <  1:21653/143‑1 (MQ=255)

                                          aTCGCCGCAGAGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGCTCAGGTTCCGCGGATCCCGAACAAACGGTCTCAACCAGTTAAGGCACGCCGACAGGAAATTAGCCCCGCAAAAGGGGccgt                                                                                       >  2:131327/1‑140 (MQ=255)

                                          aTCGCCGAAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCCGATCAGGATCCACGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCAGACAAGAAATCACCCCCGCAAATGGGTCAtg                                                                                       >  2:59746/1‑142 (MQ=255)

                                              ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGACCAGGTTCCGCGGAGCCCGAATAAACGGTCTCCACCAGGTAAGGCACCCCGACAAGAAATGCGCCCCGCAAATGGAGCAtccaac                                                                                   >  2:75120/1‑138 (MQ=255)

                                                         atgcgatAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAACCGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTTAATGTAAATTAcgc                                                                        >  2:121562/1‑143 (MQ=255)

                                                         atgcgatAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAATGAATGGACATTAcgc                                                                        >  2:488811/1‑143 (MQ=255)

                                                                  cAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTa                                                                                                          <  1:451714/100‑1 (MQ=255)

                                                                  cAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTa                                                                                                          >  2:451714/1‑100 (MQ=255)

                                                                     cttAACTCTTGTTCCCTTCTCACGTATTAGCCTGATCAGGTTCTGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGCATGTAAATTACGCGTTAACAGCGCa                                                            <  2:401108/142‑1 (MQ=255)

                                                                          ctctTGTTCCCTTCGCAGGTATTAGCGTGATCAGGTTCCGCGGAAACCAAATAAGCGGCCTCATCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACt                                                       <  2:291585/143‑1 (MQ=255)

                                                                           tctTGTTCCCTTCGCAGGTATTAGCCAGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGCGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTc                                                      >  2:626342/1‑143 (MQ=255)

                                                                            ctTGTTCCCTCCGAACGTCATAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCa                                                     <  2:103275/143‑1 (MQ=255)

                                                                                ttCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCTGACAAGAAATTAGCCCAGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa                                                 <  1:637952/143‑1 (MQ=255)

                                                                                   ccTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTACGACAAGAAATTAGCCCCGCAAATGGGGCATTGACTGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGa                                              >  2:284207/1‑143 (MQ=255)

                                                                                    gtgggCAGGTGTTAGCCTGATCGGGTTCCGGAGAGCCCGAATAAACGGGGTCGGCCAGTTAAGGCGTGCCGGCAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAGTTACGCGTTAACAGCGCAGAACTCAAGCAGGAt                                             <  2:8241/139‑1 (MQ=255)

                                                                                    cTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATGGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAt                                             >  1:53121/1‑143 (MQ=255)

                                                                                       cGCCGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAACCGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGtt                                          <  1:318409/143‑1 (MQ=255)

                                                                                        gCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGttt                                         <  1:396188/143‑1 (MQ=255)

                                                                                          aGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGa                                       <  2:388765/143‑1 (MQ=255)

                                                                                           ggTATTTGCCTGATCAGGTTCCGCTGCTCCCGAATAGACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGAc                                      <  2:199605/143‑1 (MQ=255)

                                                                                           ggTATTAGCCTGATCAGGTGCGGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGAc                                      <  1:407577/143‑1 (MQ=255)

                                                                                             tATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCACGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGAcgc                                    >  1:219909/1‑143 (MQ=255)

                                                                                                        tCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCCGGCGGCGTCa                         >  2:24684/1‑143 (MQ=255)

                                                                                                         cAGGTTCCGCGGATCCCGAATAAACGGGCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCCGCCCGCGTCaa                        <  2:285565/143‑1 (MQ=255)

                                                                                                          aGGTTCCGCGGATCCCGAATAAACGGTCTCACCCAGTTCCGGCTCTGCTACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAg                       <  1:276274/143‑1 (MQ=255)

                                                                                                            gTTCCGCGGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCa                     >  1:35710/1‑143 (MQ=255)

                                                                                                               ccGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACca                  <  1:81462/143‑1 (MQ=255)

                                                                                                                 gcgGATCCCGAATAAACGGTCTCAACCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAAGGGGGCGTTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGGCGCGGGCGGCGTCAAGCACcagc                >  1:93478/1‑143 (MQ=255)

                                                                                                                       cccGAAGAACCGGTCTCAACCAGTTAAGGCAGTGCGATAAGAAATTGGCGCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAATc          <  2:656243/143‑1 (MQ=255)

                                                                                                                         cGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAATCAg        >  2:333281/1‑143 (MQ=255)

                                                                                                                               aaCGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAATCAGCTTATc  <  1:488811/143‑1 (MQ=255)

TTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAATCAGCTTATC  >  NC_000913/4196116‑4196385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A