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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	472,742	(G)_6→7	coding (145/339 nt)	glnK →	nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	472,736	1	.	G	100.0%	135.4 / NA	38	R47G (CGG→GGG)	glnK	nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (22/16); total (22/16)

AGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAA  >  NC_000913/472602‑472866

aGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gggg                                                                                                                                >  1:714273/1‑139 (MQ=255)

aGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gggg                                                                                                                                <  1:685526/139‑1 (MQ=255)

aGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gggg                                                                                                                                <  2:505214/139‑1 (MQ=255)

aGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gggg                                                                                                                                <  1:418381/139‑1 (MQ=255)

    ggTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gggggggc                                                                                                                            >  1:468015/1‑137 (MQ=255)

     gTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gggggggcg                                                                                                                           >  1:474181/1‑136 (MQ=255)

        aCCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGaa                                                                                                                         >  1:953373/1‑139 (MQ=255)

            tGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACa                                                                                                                     <  2:420033/139‑1 (MQ=255)

             gATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAg                                                                                                                    <  1:973342/139‑1 (MQ=255)

                          ttCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTg                                                                                                       >  2:728429/1‑139 (MQ=255)

                                    aaGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTaa                                                                                             >  2:285344/1‑139 (MQ=255)

                                         gTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAAtt                                                                                        >  2:256565/1‑139 (MQ=255)

                                                   cGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGa                                                                              <  2:999715/139‑1 (MQ=255)

                                                                  gTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAAc                                                               >  1:597124/1‑139 (MQ=255)

                                                                    aTTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTc                                                             >  2:282064/1‑139 (MQ=255)

                                                                        aGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATg                                                         <  1:256565/139‑1 (MQ=255)

                                                                          ggCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGaa                                                       <  1:285344/139‑1 (MQ=255)

                                                                            ccTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGt                                                     <  1:282064/139‑1 (MQ=255)

                                                                              tGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGa                                                   <  2:597124/139‑1 (MQ=255)

                                                                              tGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGa                                                   <  1:572276/139‑1 (MQ=255)

                                                                               gACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGAt                                                  >  1:14014/1‑139 (MQ=255)

                                                                                aCCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCa                                                                 <  2:1115216/123‑1 (MQ=255)

                                                                                aCCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCa                                                                 >  1:1115216/1‑123 (MQ=255)

                                                                                aCCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATc                                                 >  1:145667/1‑139 (MQ=255)

                                                                                 ccGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCg                                                <  2:14014/139‑1 (MQ=255)

                                                                                    tCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAGTTGATCGat                                              >  1:711242/1‑138 (MQ=255)

                                                                                    tCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAGGTGATCGat                                              <  2:711242/138‑1 (MQ=255)

                                                                                          aaGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCa                                       >  2:20335/1‑139 (MQ=255)

                                                                                           aGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAg                                      >  2:835978/1‑139 (MQ=255)

                                                                                            gTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑ggggggg                                                                                                                             <  2:90145/50‑2 (MQ=255)

                                                                                            gTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑ggggggg                                                                                                                             >  1:90145/1‑49 (MQ=255)

                                                                                             tGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTa                                    <  1:20335/139‑1 (MQ=255)

                                                                                                     ttCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACa                                                                                                                     >  1:214284/1‑50 (MQ=255)

                                                                                                     ttCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACa                                                                                                                     <  2:214284/50‑1 (MQ=255)

                                                                                                     ttCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCt                                                                         <  1:159499/94‑1 (MQ=255)

                                                                                                     ttCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCt                                                                         >  2:159499/1‑94 (MQ=255)

                                                                                                                    gggCATGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAAtt             >  2:320809/1‑139 (MQ=255)

                                                                                                                        aTGCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCg         <  1:728429/139‑1 (MQ=255)

                                                                                                                           ccGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAgg                                 >  2:1103940/1‑112 (MQ=255)

                                                                                                                           ccGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAgg                                 <  1:1103940/112‑1 (MQ=255)

                                                                                                                           ccGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACg      >  2:365580/1‑139 (MQ=255)

                                                                                                                           ccGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACg      >  2:313207/1‑139 (MQ=255)

                                                                                                                           ccGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTCCCAAAAGTAGAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACg      >  2:686384/1‑139 (MQ=255)

                                                                                                                               gCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCaa  >  2:518282/1‑139 (MQ=255)

                                                                                                                               gCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCaa  >  2:568978/1‑139 (MQ=255)

                                                                                                                               gCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCaa  >  2:810883/1‑139 (MQ=255)

AGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAA  >  NC_000913/472602‑472866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A