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
A9 F1 I1 R1	759	71.0	3673240	91.5%	3361014	104.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,966,188	C→T	749 (TAG→TAA)	ptsP ←	PEP‑protein phosphotransferase enzyme I, GAF domain containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,966,188	0	C	T	100.0%	176.5 / NA	55	749 (TAG→TAA)	ptsP	PEP‑protein phosphotransferase enzyme I, GAF domain containing protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (30/25); total (30/25)

TTATTTCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGCTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATGCGC  >  NC_000913/2966057‑2966323

ttATTTCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAAcc                                                                                                                                  <  2:1666916/139‑1 (MQ=255)

     tCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAAcc                                                                                                                                  >  2:823983/1‑134 (MQ=255)

     tCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAAcc                                                                                                                                  <  1:823983/134‑1 (MQ=255)

     tCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCcg                                                                                                                             >  2:1779089/1‑139 (MQ=255)

     tCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCcg                                                                                                                             >  2:455788/1‑139 (MQ=255)

          gAAAGAGAACAGGGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAAt                                                                                                                        <  1:118225/139‑1 (MQ=255)

                            aaaTGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACC‑‑CCGCGAATCAGCCCGCCCATGCCGCGAc                                                                                                    <  2:328111/139‑1 (MQ=255)

                                   tgccgcAGGTCTCAGGCGCTCCAAAGGTGCGAATAATAGCATAAGGGGACCTTGCCGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTcc                                                                                               >  1:432781/2‑139 (MQ=255)

                                       gcAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATaa                                                                                           <  1:455788/139‑1 (MQ=255)

                                       gcAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATaa                                                                                           <  1:1779089/139‑1 (MQ=255)

                                             ttCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTg                                                                                     >  2:328058/1‑139 (MQ=255)

                                                       ccAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATg                                                                           >  1:1722768/1‑139 (MQ=255)

                                                                cGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTc                                                                  >  2:1407210/1‑139 (MQ=255)

                                                                cGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTc                                                                  >  2:1549620/1‑139 (MQ=255)

                                                                       taGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACg                                                                                                   >  2:638402/1‑99 (MQ=255)

                                                                       taGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACg                                                                                                   <  1:638402/99‑1 (MQ=255)

                                                                       taGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGcc                                                           >  1:488176/1‑139 (MQ=255)

                                                                       taGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGcc                                                           >  2:784160/1‑139 (MQ=255)

                                                                                 ggACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCtt                                                 <  1:328058/139‑1 (MQ=255)

                                                                                  gACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGc                                                                                                  >  2:146781/1‑89 (MQ=255)

                                                                                  gACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGc                                                                                                  <  1:146781/89‑1 (MQ=255)

                                                                                   aCCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTcc                                               <  1:1407210/139‑1 (MQ=255)

                                                                                      tggctggTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGa                                            <  2:488176/139‑1 (MQ=255)

                                                                                       ggctggTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATaa                                                                                           <  2:1018352/91‑1 (MQ=255)

                                                                                       ggctggTTGCCGGATACCATTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATaa                                                                                           >  1:1018352/1‑91 (MQ=255)

                                                                                               gCCGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTgc                                   <  1:1549620/139‑1 (MQ=255)

                                                                                                 cGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAgcccgcc                                                                                                               <  1:884129/61‑1 (MQ=255)

                                                                                                 cGGATACCGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAgcccgcc                                                                                                               >  2:884129/1‑61 (MQ=255)

                                                                                                       ccGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCg                                                                 >  1:1673500/1‑101 (MQ=255)

                                                                                                       ccGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCg                                                                 <  2:1673500/101‑1 (MQ=255)

                                                                                                        cGTTAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGAttt                          >  2:1724404/1‑139 (MQ=255)

                                                                                                          ttAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCtt                                                 <  1:1174220/114‑1 (MQ=255)

                                                                                                          ttAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCtt                                                 >  2:1174220/1‑114 (MQ=255)

                                                                                                          ttAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACg                                       <  1:1750311/124‑1 (MQ=255)

                                                                                                          ttAAAAGATATGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACg                                       >  2:1750311/1‑124 (MQ=255)

                                                                                                                  tatGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGa                                                                                                     >  2:342807/1‑54 (MQ=255)

                                                                                                                  tatGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGa                                                                                                     <  1:342807/54‑1 (MQ=255)

                                                                                                                   atGTATATGATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGc               <  2:1722768/139‑1 (MQ=255)

                                                                                                                           gATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATaa                                                                                           >  2:747999/1‑55 (MQ=255)

                                                                                                                           gATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATaa                                                                                           <  1:747999/55‑1 (MQ=255)

                                                                                                                           gATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCaa       >  2:836247/1‑139 (MQ=255)

                                                                                                                           gATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCaa       >  1:1732196/1‑139 (MQ=255)

                                                                                                                           gATCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCaa       >  2:245739/1‑139 (MQ=255)

                                                                                                                             tCCGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATg     >  2:1762031/1‑139 (MQ=255)

                                                                                                                              ccGCGTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgc    >  2:812136/1‑139 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCcg                                                                                                        <  1:728370/38‑1 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCcg                                                                                                        >  2:728370/1‑38 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAgg                                                                                        <  2:1725977/54‑1 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAgg                                                                                        >  1:1725977/1‑54 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCTGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCgg                <  2:1199975/126‑1 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcg   >  1:1363234/1‑139 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcg   <  2:1652406/139‑1 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcg   >  1:329198/1‑139 (MQ=255)

                                                                                                                               cgcgTTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcg   <  1:784160/139‑1 (MQ=255)

                                                                                                                               cgcgTTAAAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTACTTCgg                >  1:1199975/1‑126 (MQ=255)

                                                                                                                                gcgtTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcgc  >  1:1736220/1‑139 (MQ=255)

                                                                                                                                gcgtTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcgc  >  2:456593/1‑139 (MQ=255)

                                                                                                                                gcgtTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATgcgc  >  2:226259/1‑139 (MQ=255)

TTATTTCGCTGAAAGAGAACAGCGATTGAAATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTGCGAATAATAGCACAAGGGGACCTGGCTGGTTGCCGGATACCGTTAAAAGATATGTATATGATCCGCGCTATAACCCTCCGCGAATCAGCCCGCCCATGCCGCGACGCTCCATAAAGGCTGCAACCTGATGGCGAACTTCGGTCGCCAGTTGCGCTTCCAGACTACGCTGCGCAAGATTTTCTGCTTCGGCATAATCAATGCGC  >  NC_000913/2966057‑2966323

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A