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	3,347,069	G→A	164 (TAG→TAA)	ptsN →	sugar‑specific enzyme IIA component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,347,069	0	G	A	100.0%	118.8 / NA	38	164 (TAG→TAA)	ptsN	sugar‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/16); total (22/16)

CCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTGG  >  NC_000913/3346937‑3347202

ccTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTc                                                                                                                                 <  1:712432/139‑1 (MQ=255)

        ctctGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                         <  2:53933/139‑1 (MQ=255)

        ctctGTCGCTGGTGGCGAAACGACTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGAATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                         <  2:22081/139‑1 (MQ=255)

           tGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGtctc                                                                                                                      >  1:665453/1‑139 (MQ=255)

             tCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCtt                                                                                                                    >  1:549594/1‑139 (MQ=255)

                 tggtggCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAg                                                                                                                <  2:795419/139‑1 (MQ=255)

                            cGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                     <  1:237330/139‑1 (MQ=255)

                                      aCAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                   <  2:357499/131‑1 (MQ=255)

                                      aCAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                   >  1:357499/1‑131 (MQ=255)

                                      aCAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTa                                                                                           <  1:786940/139‑1 (MQ=255)

                                        aaaaCCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACa                                                                                         <  2:549594/139‑1 (MQ=255)

                                                               cgcAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGa                                                                  <  2:665453/139‑1 (MQ=255)

                                                                  aGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACgt                                                               >  2:150879/1‑139 (MQ=255)

                                                                   gCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGt                                                                                            <  1:599145/109‑1 (MQ=255)

                                                                   gCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGt                                                                                            >  2:599145/1‑109 (MQ=255)

                                                                              tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                         >  1:578466/1‑69 (MQ=255)

                                                                              tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                         <  2:578466/69‑1 (MQ=255)

                                                                              tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCttt                                                                                                                   >  1:580426/1‑75 (MQ=255)

                                                                              tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCttt                                                                                                                   <  2:580426/75‑1 (MQ=255)

                                                                                             aaTCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACa                                                                                              <  1:403493/81‑1 (MQ=255)

                                                                                             aaTCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACa                                                                                              >  2:403493/1‑81 (MQ=255)

                                                                                             aaTCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtg                                    >  2:449642/1‑139 (MQ=255)

                                                                                                 aTTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtg                                <  2:530784/139‑1 (MQ=255)

                                                                                                  ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtgc                               >  2:324315/1‑139 (MQ=255)

                                                                                                    aCGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                                <  1:741613/72‑1 (MQ=255)

                                                                                                    aCGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                                >  2:741613/1‑72 (MQ=255)

                                                                                                    aCGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTgcgc                             >  2:146671/1‑139 (MQ=255)

                                                                                                          aCCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAg                       >  2:798513/1‑139 (MQ=255)

                                                                                                              aaGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGata                    <  1:72482/138‑1 (MQ=255)

                                                                                                              aaGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGata                    >  2:72482/1‑138 (MQ=255)

                                                                                                                    cTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGttt             >  1:121482/1‑139 (MQ=255)

                                                                                                                      ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGttttt           >  2:318740/1‑139 (MQ=255)

                                                                                                                           tGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGc      >  1:243350/1‑139 (MQ=255)

                                                                                                                            gAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCg     >  1:781045/1‑139 (MQ=255)

                                                                                                                              aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTg   >  2:338673/1‑139 (MQ=255)

                                                                                                                              aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTg   >  2:332970/1‑139 (MQ=255)

                                                                                                                              aGCGTAATTATTCGGGAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCGGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTg   >  1:537148/1‑139 (MQ=255)

                                                                                                                               gCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTgg  >  2:683927/1‑139 (MQ=255)

CCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTGG  >  NC_000913/3346937‑3347202

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