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	1,212,703	C→T	135 (TAG→TAA)	ycgX ←	DUF1398 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,212,703	0	C	T	100.0%	95.2 / NA	31	135 (TAG→TAA)	ycgX	DUF1398 family protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/15); total (16/15)

TCTGGTGATTATTTATGGGTGACAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGCTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGCCAGTGTTG  >  NC_000913/1212572‑1212830

tCTGGTGATTATTTATGGGTGACAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          >  1:325151/1‑139 (MQ=255)

    gTGATTATTTATGGGTGACAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          >  1:271723/1‑135 (MQ=255)

    gTGATTATTTATGGGTGACAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          <  2:271723/135‑1 (MQ=255)

              atGGGTGACAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTAttt                                                                                                            >  1:971597/1‑139 (MQ=255)

                     aCAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACAt                                                                                                     >  2:441598/1‑139 (MQ=255)

                      cAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTtta                                                                                                                  <  2:574669/125‑1 (MQ=255)

                      cAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTtta                                                                                                                  >  1:574669/1‑125 (MQ=255)

                        aTAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCtt                                                                                                  <  2:971597/139‑1 (MQ=255)

                          aaaaaGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCa                                                                                                <  1:441598/139‑1 (MQ=255)

                                   gTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATaaa                                                                                       <  1:954456/139‑1 (MQ=255)

                                              ccATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATaaa                                                                                       <  1:986902/128‑1 (MQ=255)

                                              ccATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATaaa                                                                                       >  2:986902/1‑128 (MQ=255)

                                                        aGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          >  1:933000/1‑83 (MQ=255)

                                                        aGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          <  2:933000/83‑1 (MQ=255)

                                                        aGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCgtag                                                                  >  1:1089142/1‑139 (MQ=255)

                                                        aGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCg                                                                     <  1:941750/136‑1 (MQ=255)

                                                        aGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCg                                                                     >  2:941750/1‑136 (MQ=255)

                                                                     ttATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTAttt                                                                                                            >  1:1107043/1‑84 (MQ=255)

                                                                     ttATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTAttt                                                                                                            <  2:1107043/84‑1 (MQ=255)

                                                                       aTTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTa                                                   <  2:1089142/139‑1 (MQ=255)

                                                                                      aTGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTa                                    >  1:978496/1‑139 (MQ=255)

                                                                                             aCTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          >  1:524554/1‑46 (MQ=255)

                                                                                             aCTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGTTAGATTa                                                                                                                          <  2:524554/46‑1 (MQ=255)

                                                                                                           cATTTCTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCcgcg               >  1:843259/1‑139 (MQ=255)

                                                                                                                cTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGc          <  2:843259/139‑1 (MQ=255)

                                                                                                                cTTAAGTATCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGc          <  2:978496/139‑1 (MQ=255)

                                                                                                                        tCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGtt                                                    >  2:477874/1‑89 (MQ=255)

                                                                                                                        tCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGtt                                                    <  1:477874/89‑1 (MQ=255)

                                                                                                                        tCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGc          >  2:419601/1‑131 (MQ=255)

                                                                                                                        tCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGc          <  1:419601/131‑1 (MQ=255)

                                                                                                                        tCCAACTTTAGTTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGCCAGTGTTg  >  2:408486/1‑139 (MQ=255)

TCTGGTGATTATTTATGGGTGACAATAAAAAGACAGTATTAATCATCCATAGAGATAGTCTCTGCACTTTTATTTCCATTATGCTAATGCCTTACTGAATTATGAAGCATTTCTTAAGTATCCAACTTTAGCTAGATTAATGGTTTATTATTTTCTACATCTTCAATATATAAAAGCGTATTATCAATGGCGTAGTAACTGCGTTTGTTATGATTAACATCAGTAACCCACCGGAAAACGCCCGCGCCTGCCAGTGTTG  >  NC_000913/1212572‑1212830

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