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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,792,267	C→T	155 (TAG→TAA)	nlpC ←	putative C40 clan peptidase lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,792,267	0	C	T	95.2%	61.3 / ‑5.8	21	155 (TAG→TAA)	nlpC	putative C40 clan peptidase lipoprotein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (9/11); minor base A (0/1); total (9/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATACTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTAAATACCTACATGCAA  >  NC_000913/1792159‑1792392

ccTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTc                                                                                                 <  1:1071241/139‑1 (MQ=255)

     ttATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCa                                                                                            <  2:584433/139‑1 (MQ=255)

                       tttACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGa                                                                                                                           >  1:1034869/1‑90 (MQ=255)

                       tttACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGa                                                                                                                           <  2:1034869/90‑1 (MQ=255)

                                                    ctGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGa                                                                                                                           <  1:256483/61‑1 (MQ=255)

                                                    ctGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGa                                                                                                                           >  2:256483/1‑61 (MQ=255)

                                                       tATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCa                                                                                            >  2:849934/1‑89 (MQ=255)

                                                       tATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCa                                                                                            <  1:849934/89‑1 (MQ=255)

                                                                 tAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATc                                                                                >  2:695008/1‑91 (MQ=255)

                                                                 tAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATc                                                                                <  1:695008/91‑1 (MQ=255)

                                                                   aaTGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTa                                                 <  2:914506/120‑1 (MQ=255)

                                                                   aaTGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTa                                                 >  1:914506/1‑120 (MQ=255)

                                                                              aTGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTccc                                                          >  1:854617/1‑100 (MQ=255)

                                                                              aTGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTccc                                                          <  2:854617/100‑1 (MQ=255)

                                                                                      tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCtt                                                        <  2:420842/94‑1 (MQ=255)

                                                                                      tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCtt                                                        >  1:420842/1‑94 (MQ=255)

                                                                                         ccGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGa                                                                                       >  1:818769/1‑60 (MQ=255)

                                                                                         ccGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGa                                                                                       <  2:818769/60‑1 (MQ=255)

                                                                                         ccGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCa                                                               <  2:338591/84‑1 (MQ=255)

                                                                                         ccGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCa                                                               >  1:338591/1‑84 (MQ=255)

                                                                                               aattttCGACCAAATAGAATCGGCCTGCCTGCCAGAAATTTTTCTTCCAATTATCATTATCCAATTAAGAACGCCTCACCCCCTTTCTGGTAAAGGCGTGGATAAAATGGTTGTTGGTATCGTAAATACCTACATGCaa  <  1:630265/137‑1 (MQ=255)

CCTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATACTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTAAATACCTACATGCAA  >  NC_000913/1792159‑1792392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A