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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,863	C→T	pseudogene (19/48 nt)	rph ←	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,863	0	C	T	100.0%	70.5 / NA	23	pseudogene (19/48 nt)	rph	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (11/12); total (11/12)

CGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGT  >  NC_000913/3815733‑3815997

cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGga                                                                                                                               <  1:354159/139‑1 (MQ=255)

       tCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                        <  2:5234/139‑1 (MQ=255)

                 ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                              <  1:318074/139‑1 (MQ=255)

                            ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAAt                                                                                                                                  >  1:335518/1‑108 (MQ=255)

                            ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAAt                                                                                                                                  <  2:335518/108‑1 (MQ=255)

                                 cATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                              <  2:210047/139‑1 (MQ=255)

                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACa                                                                                                                                    >  1:206644/1‑100 (MQ=255)

                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGa                                                                                             >  2:17813/1‑139 (MQ=255)

                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTGAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACa                                                                                                                                    <  2:206644/100‑1 (MQ=255)

                                    gCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                                                                             <  1:150372/105‑1 (MQ=255)

                                    gCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                                                                             >  2:150372/1‑105 (MQ=255)

                                                                             gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTTGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca                                                                                                      <  1:119009/88‑1 (MQ=255)

                                                                             gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTTGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca                                                                                                      >  2:119009/1‑88 (MQ=255)

                                                                                 cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACt                                              >  1:755804/1‑139 (MQ=255)

                                                                                       aGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatg                                        >  1:38329/1‑139 (MQ=255)

                                                                                           gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                              >  2:373670/1‑82 (MQ=255)

                                                                                           gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                              <  1:373670/82‑1 (MQ=255)

                                                                                                aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCg                               >  2:22270/1‑139 (MQ=255)

                                                                                                       aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                        >  1:144971/1‑44 (MQ=255)

                                                                                                       aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                        <  2:144971/44‑1 (MQ=255)

                                                                                                              cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                 <  1:22270/139‑1 (MQ=255)

                                                                                                                             cgtcgtTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt  >  2:795496/1‑139 (MQ=255)

                                                                                                                              gTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                         <  1:730788/115‑1 (MQ=255)

                                                                                                                              gTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                         >  2:730788/1‑115 (MQ=255)

CGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGT  >  NC_000913/3815733‑3815997

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A