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
A27 F124 I1 R1	28	40.1	1601150	89.4%	1431428	142.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,196,204	G→A	intergenic (‑105/+128)	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	4,196,204	0	G	A	100.0%	150.1 / NA	47	intergenic (‑105/+128)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/23); total (24/23)

TCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAT  >  NC_000913/4196071‑4196342

tCGCGGCGGGTCAGTTTTGTTGCAGACCTAAATCGTATAAGGAGGTTGTGTGTGTGGCTTGTCCGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTa                                                                                                                                   >  1:547720/1‑143 (MQ=255)

tCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTa                                                                                                                                   >  1:541969/1‑143 (MQ=255)

 cgcgGCGGGTCAGTTTTGTTGCAGACATCGCTCATTCCAACAAGTTAAGGACGTGGCTTGTCAGACGACGGATGGAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTGTTAg                                                                                                                                  >  2:416536/1‑143 (MQ=255)

  ggggcggGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGc                                                                                                                                 <  1:476153/141‑1 (MQ=255)

        ggTCAGTTTTGTTGCAGACATCGCTCATTCCAAAATGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATc                                                                                                                           <  1:158209/143‑1 (MQ=255)

           cAGTTTTGTTGCAGACATAGCTCATTCCAAACAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAgg                                                                                                                        <  1:654562/143‑1 (MQ=255)

           cAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAgg                                                                                                                        <  1:686456/143‑1 (MQ=255)

                    tgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGa                                                                                                               <  1:395280/143‑1 (MQ=255)

                      cAGACATAGCGCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATc                                                                                                             <  2:25755/143‑1 (MQ=255)

                       aGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTGCCCTTCACAGGTATTAGCCTGATCAGGCTCCGCGGATcc                                                                                                            >  2:537988/1‑143 (MQ=255)

                        gACATAGCAGAGTCCGAAAAGCTAAGGACGGGGCGGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTCACAGGGATTAGCCTGATCAGGTTCCGCGGATccc                                                                                                           <  1:631111/143‑1 (MQ=255)

                                tCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGAACGCTTCAGGTGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGACTAAAc                                                                                                   >  1:217986/1‑143 (MQ=255)

                                 cATTCCAAAAAGTTAAGGACGTGGCTGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                                  <  2:85204/143‑1 (MQ=255)

                                      cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc                                                                                             >  1:626276/1‑143 (MQ=255)

                                       aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCa                                                                                            <  1:133256/143‑1 (MQ=255)

                                           aGTCAAGGACGTGGCTTGCCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCCTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                        <  1:39079/143‑1 (MQ=255)

                                                aGGACGTGGCTTGTCAGACGACGGATGAAGCGAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa                                                                                   <  2:530058/143‑1 (MQ=255)

                                                           tGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGCGGCGATGCGAGAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGATAAGGCACTCCGAc                                                                        >  1:185308/1‑143 (MQ=255)

                                                                 acgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGATGAGTGGCTGTTGTTGGATAGATATACGATTTCGTGGTCAGGTTCCGCGGATCACGACTAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaca                                                                  >  1:796714/1‑141 (MQ=255)

                                                                  cgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAt                                                                 <  1:485291/143‑1 (MQ=255)

                                                                          gAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCCGACCGTGAAGACACTCCGACAAGAAATTAGCCCCg                                                         >  1:539195/1‑143 (MQ=255)

                                                                          gAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCCCTCCGACAAGAAATTAGCCCCg                                                         >  1:244462/1‑143 (MQ=255)

                                                                              cAAGAGACGATCGCCGCAGGGGCGATGCGATCGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTGTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaac                                                     >  1:605076/1‑142 (MQ=255)

                                                                               aaGAGACGATCGCCGCAGGGGCGATGCGATAACAGATTAACTCTTGTTCCCTGCACAGGTATTAGACTGATCAGGTTCCGCGGATCCCGAATAAACGTTCTCAGCCAGTCAAGGCACTCCGACAAGAAATTAGACCCGCaaag                                                    >  2:652485/1‑142 (MQ=255)

                                                                                      gATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCCGTTCAGGCACTCCGCCAAGAAATTAGCCCCGCAAAAGGAGCAt                                             >  1:487880/1‑143 (MQ=255)

                                                                                       agcgccgcCGGGGCGACGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt                                            <  1:118142/141‑1 (MQ=255)

                                                                                         cgccgcACGGGCGATTCAATAGCATATTAACTCTTGTTCCCTTCACACGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGa                                          <  1:4540/143‑1 (MQ=255)

                                                                                          gccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                         <  1:437997/143‑1 (MQ=255)

                                                                                           ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCGCCGCAACTGGGGCATTGAAt                                        >  1:163057/1‑143 (MQ=255)

                                                                                           ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                        <  1:70049/143‑1 (MQ=255)

                                                                                            cgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATg                                       <  1:41454/143‑1 (MQ=255)

                                                                                                 gggCGATGCGATAGCAGACTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGTGTTTAGCCCCGCAAATGGGGCATTGAATGTAAAt                                  <  2:654132/143‑1 (MQ=255)

                                                                                                   gcgatgcgatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGCATGTAAATTa                                >  1:782666/1‑143 (MQ=255)

                                                                                                            tAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAAGTTCCGCGGATCCCGAATAAACGGTCTCCGCCAGTTAAGGCACTCCGGCAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAAc                       >  2:471377/1‑143 (MQ=255)

                                                                                                             aGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTACGGCACTCCGACAAGAAATTAGCCCCGCAAATGGTGCTTTTCCTGTAACTTAGGCGGCAACa                      >  1:230433/1‑143 (MQ=255)

                                                                                                                 gATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCCCTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAgcgc                  >  1:553172/1‑143 (MQ=255)

                                                                                                                  aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCGAATGGGGCATTGAATGTAAATTACGCTGTAACAgcgaa                 >  2:374861/1‑141 (MQ=255)

                                                                                                                  aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAGATGGGGCATTGAATATAAATTACGCGTTAACAGCGCa                 >  1:292519/1‑143 (MQ=255)

                                                                                                                  aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                 <  2:541969/143‑1 (MQ=255)

                                                                                                                  aTTAACTCGTGTTCCCGTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGTCAGTTACGGCACTCCTACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                 <  1:247922/143‑1 (MQ=255)

                                                                                                                  aTTAACTCCTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                 <  2:547720/143‑1 (MQ=255)

                                                                                                                   ttAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGGAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAg                >  1:657068/1‑143 (MQ=255)

                                                                                                                     aaCTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGaa              <  1:571622/143‑1 (MQ=255)

                                                                                                                       ctctTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGACCt            >  1:176313/1‑143 (MQ=255)

                                                                                                                          tcgtccccTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAACAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCaa         <  1:416536/138‑1 (MQ=255)

                                                                                                                                 cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAATTTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGGAGAACGCGAGCAGGac  >  1:737295/1‑142 (MQ=255)

                                                                                                                                 cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGGCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAt  >  1:358007/1‑143 (MQ=255)

TCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAT  >  NC_000913/4196071‑4196342

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