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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,842,931	T→C	D38G (GAC→GGC)	hycI ←	protease involved in processing C‑terminal end of HycE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,842,931	0	T	C	100.0%	113.3 / NA	34	D38G (GAC→GGC)	hycI	protease involved in processing C‑terminal end of HycE
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/18); total (16/18)

TCGGCGATATCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAA  >  NC_000913/2842796‑2843063

tcGGCGATATCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCaa                                                                                                                                   >  2:276443/1‑139 (MQ=255)

tcGGCGATATCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCaa                                                                                                                                   >  2:246968/1‑139 (MQ=255)

   gCGATATCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATca                                                                                                                                <  2:416264/139‑1 (MQ=255)

     gATATCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATcacc                                                                                                                              <  1:276443/139‑1 (MQ=255)

        atcatcCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCaccacc                                                                                                                           <  1:246968/139‑1 (MQ=255)

                 gTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCt                                                                                                                  >  1:176730/1‑139 (MQ=255)

                       gatgCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTcggc                                                                                                            >  1:510487/1‑139 (MQ=255)

                           cGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTcggcgcgg                                                                                                        <  2:789153/139‑1 (MQ=255)

                                                         gTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTg                                                                          >  1:933197/1‑139 (MQ=255)

                                                           ggCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTgcg                                                                        <  1:161977/139‑1 (MQ=255)

                                                            gCGTCGACAATCAGCAGTCCTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCCCCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTgcgc                                                                       >  2:986430/1‑139 (MQ=255)

                                                               tCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCcat                                                                    >  2:348502/1‑139 (MQ=255)

                                                                    aaTCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCg                                                               <  1:348502/139‑1 (MQ=255)

                                                                             tCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACt                                                                                               >  1:205711/1‑98 (MQ=255)

                                                                             tCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACt                                                                                               <  2:205711/98‑1 (MQ=255)

                                                                               gtgtCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCt                                                    <  2:176730/139‑1 (MQ=255)

                                                                                tgtCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTa                                                   >  2:478543/1‑139 (MQ=255)

                                                                                tgtCGGGCGCAGTTCACGAATGGCTACGATGTCGTTTTCCGGTGCCATACCGCCCCCAATCCCCACCCAGTTACCTTTCGGCCGGGACGCGCACTTTTCCTCCAGCAGCGGACCTGCGCCATCATCTCCAAGCATGCTa                                                   >  1:681083/1‑139 (MQ=255)

                                                                                    gggCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGc                                               <  1:478543/139‑1 (MQ=255)

                                                                                       cgcAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTcggcg                                                                                                           >  2:356768/1‑76 (MQ=255)

                                                                                       cgcAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTcggcg                                                                                                           <  1:356768/76‑1 (MQ=255)

                                                                                       cgcAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCaa                                            >  1:916299/1‑139 (MQ=255)

                                                                                           gTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAAcaca                                        <  1:518597/139‑1 (MQ=255)

                                                                                           gTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAAcaca                                        <  1:85871/139‑1 (MQ=255)

                                                                                                      gCGACGATGTCGTTTTCCGGTGGGCTACTGCCGCTAATCACCACCCAGTAACCTTTCGGCGGGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACgt                             >  1:654206/1‑139 (MQ=255)

                                                                                                      gCGACGATGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACgt                             >  2:215166/1‑139 (MQ=255)

                                                                                                       cgacgaTGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCt                                                    >  1:902347/1‑115 (MQ=255)

                                                                                                       cgacgaTGTCGTTTTCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCt                                                    <  2:902347/115‑1 (MQ=255)

                                                                                                                  ttttCCGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGt                 <  2:510487/139‑1 (MQ=255)

                                                                                                                      ccGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTctcc             <  2:933197/139‑1 (MQ=255)

                                                                                                                       cGGTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTctcct            <  2:762050/139‑1 (MQ=255)

                                                                                                                         gTGCGCTACCGCCGCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCa          <  2:916299/139‑1 (MQ=255)

                                                                                                                                 ccgccgCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATaaaa  >  2:652010/1‑139 (MQ=255)

                                                                                                                                    ccgCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCcat                                                                    <  1:978651/70‑1 (MQ=255)

                                                                                                                                    ccgCCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCcat                                                                    >  2:978651/1‑70 (MQ=255)

TCGGCGATATCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATCACCACCCAGTTACCTTTCGGCGCGGCGGCGCACTTTTCCGCCAGCAGCGGACCTGCGCCATCATCGCCCATCATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAA  >  NC_000913/2842796‑2843063

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A