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
A11 F83 I1 R1	24	40.7	1567444	90.4%	1416969	141.3

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%	147.7 / 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 (26/21); total (26/21)

GCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATG  >  NC_000913/4196073‑4196343

gcggcgGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGc                                                                                                                                  <  1:219401/143‑1 (MQ=255)

gcggcgGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGc                                                                                                                                  >  2:704525/1‑143 (MQ=255)

       gTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCa                                                                                                                           <  1:320033/143‑1 (MQ=255)

              ttgttgCAGACATAGCTCATTCCAAAAAGTTAAGTACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCcg                                                                                                                    <  2:620015/143‑1 (MQ=255)

                             cTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGCGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGCATaaa                                                                                                     >  2:591860/1‑143 (MQ=255)

                              tCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGCCGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAAc                                                                                                    >  1:506088/1‑143 (MQ=255)

                               cATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                                   <  1:175511/143‑1 (MQ=255)

                               cATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                                   <  1:556161/143‑1 (MQ=255)

                                   ccAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtct                                                                                               <  1:193955/143‑1 (MQ=255)

                                    cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc                                                                                              >  1:350290/1‑143 (MQ=255)

                                    cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc                                                                                              >  1:425893/1‑143 (MQ=255)

                                     aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCCGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAAAAAACGGCCTCa                                                                                             >  2:102326/1‑143 (MQ=255)

                                     aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGAACCCGAATAAACGGACTCa                                                                                             >  2:72503/1‑143 (MQ=255)

                                      aaaaGTTAAGGACGTGTCTTGTCAGTCGACGGATGAAGCAAGATACGATCGCCGCAGGGGCGATGCTATAGCAGATTAACTCTTGTTCCCTTCACATGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAg                                                                                            <  2:379101/143‑1 (MQ=255)

                                         aGTTAGGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCGGGGGCGATGCGATAGCAGATGAACTCTTGTTCCCTTCACAGGCATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                         <  2:231650/143‑1 (MQ=255)

                                                 aCGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTGTTGTTCCCTTCACAGGTATAAGCCTGATCAGGTTCCGCGGATCCAGAAGAAACGGTCACAGCCAggcaacgc                                                                                 >  2:330784/1‑136 (MQ=255)

                                                     ggCTTGTCAGACGACGGACGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTc                                                                             <  1:199765/143‑1 (MQ=255)

                                                      gCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTcc                                                                            >  1:747658/1‑143 (MQ=255)

                                                         tGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGAc                                                                         <  2:643253/143‑1 (MQ=255)

                                                          gTCAGACCACGGATCAAGCAAGCGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTCACAGGCATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACa                                                                        <  1:190801/143‑1 (MQ=255)

                                                             aGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAGGGCACTCCGACAAGa                                                                     >  1:489212/1‑143 (MQ=255)

                                                                 gacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAtt                                                                 >  1:200127/1‑143 (MQ=255)

                                                                         aaGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGc                                                         >  1:344236/1‑143 (MQ=255)

                                                                           gCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaa                                                       >  1:607640/1‑143 (MQ=255)

                                                                            cAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCCGATCAGGTTCCGCAGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaaa                                                      <  2:389466/143‑1 (MQ=255)

                                                                               gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa                                                                                                     >  2:52860/1‑93 (MQ=255)

                                                                               gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa                                                                                                     <  1:52860/93‑1 (MQ=255)

                                                                                 gaCGATCGCCGCAGGGGCGATGCGATAGCAGATGAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATgggg                                                 <  2:619185/143‑1 (MQ=255)

                                                                                         ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCCAATGGGGCATTGAAt                                         >  1:342953/1‑143 (MQ=255)

                                                                                         ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                         <  1:554150/143‑1 (MQ=255)

                                                                                              ggggggATGCGTTGGCTGATTAACTGTTGTTCCCTTCATAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTaaa                                    <  2:136494/143‑1 (MQ=255)

                                                                                               gggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAAt                                   <  2:779932/143‑1 (MQ=255)

                                                                                                     tgcgatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgcg                             >  1:308080/1‑143 (MQ=255)

                                                                                                       cgatAGTCGATTAAGTCTTGTCCCATTCACACGTATTAGCCTGATCAGGTTCAGAGGCTCCCGAATAAACGGTCTCAGCCAGTTAAGCCACCCCGACAACACACTCGCCCCGCAAATGCGGCATTGAATGTAAATTACGCGtt                           <  2:132212/143‑1 (MQ=255)

                                                                                                        gatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCAGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAGTAGCCCCGCAAATGGGGCATGGAATGTAAATAACGCGATa                          >  2:618704/1‑143 (MQ=255)

                                                                                                            gCAGACTACCTCTTGTTCCCTTCACAGGTCTTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAg                      <  1:83297/143‑1 (MQ=255)

                                                                                                                aTTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                  >  2:740544/1‑143 (MQ=255)

                                                                                                                 ttAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAg                 >  2:485479/1‑143 (MQ=255)

                                                                                                                    aCTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAAc              >  1:484540/1‑143 (MQ=255)

                                                                                                                           ttCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa       >  2:266273/1‑143 (MQ=255)

                                                                                                                           ttCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAAGTAGCCGCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa       >  2:725725/1‑143 (MQ=255)

                                                                                                                               cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          >  1:651434/1‑104 (MQ=255)

                                                                                                                               cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          <  2:650086/104‑1 (MQ=255)

                                                                                                                               cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          <  2:651434/104‑1 (MQ=255)

                                                                                                                               cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGaa                                          >  1:650086/1‑104 (MQ=255)

                                                                                                                               cTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACCGAAGCAggct   >  2:572396/1‑141 (MQ=255)

                                                                                                                                ttCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTCACAGCGGAGAACTCAAGCAGGATg  >  1:697782/1‑143 (MQ=255)

GCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATG  >  NC_000913/4196073‑4196343

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