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
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,000	C→T	412 (TAG→TAA)	intR ←	Rac prophage, integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,000	0	C	T	100.0%	113.4 / NA	36	412 (TAG→TAA)	intR	Rac prophage, integrase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/17); total (19/17)

TCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGC  >  NC_000913/1411866‑1412119

tCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTGTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACg                                                                                                                     >  1:572443/1‑139 (MQ=255)

      aCGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                               <  2:426167/139‑1 (MQ=255)

       cGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                                              <  1:695409/139‑1 (MQ=255)

           acgacgCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTGCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                          <  2:768279/139‑1 (MQ=255)

                         tttGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTAt                                                                                            >  1:310953/1‑139 (MQ=255)

                                       aGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCa                                                                              >  1:753096/1‑139 (MQ=255)

                                            gTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                         <  2:750287/139‑1 (MQ=255)

                                            gTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                         <  2:259376/139‑1 (MQ=255)

                                              aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       <  2:630006/139‑1 (MQ=255)

                                              aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       <  2:692551/139‑1 (MQ=255)

                                              aTTGTTCTTTCTTTCTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGTGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGATATCTGTTCGTCGTTCCTGtcatc                                                                       <  2:489991/139‑1 (MQ=255)

                                                   tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       <  2:553033/134‑1 (MQ=255)

                                                   tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       >  1:553033/1‑134 (MQ=255)

                                                   tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATcc                                                                  >  2:379937/1‑139 (MQ=255)

                                                       tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACAt                                                              >  2:731638/1‑139 (MQ=255)

                                                         tttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATAc                                                            >  2:447869/1‑139 (MQ=255)

                                                          ttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATAcc                                                           <  2:558179/139‑1 (MQ=255)

                                                                       aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATac                                              <  2:753096/139‑1 (MQ=255)

                                                                                           ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                                       >  1:495300/1‑110 (MQ=255)

                                                                                           ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                                       <  2:495300/110‑1 (MQ=255)

                                                                                           ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg                          <  1:331893/139‑1 (MQ=255)

                                                                                               ctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCTCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGcccc                      >  1:399208/1‑139 (MQ=255)

                                                                                                tGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCa                     >  1:456655/1‑139 (MQ=255)

                                                                                                   tACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                               >  1:666302/1‑46 (MQ=255)

                                                                                                   tACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                               <  2:666302/46‑1 (MQ=255)

                                                                                                     cTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                <  2:592123/139‑1 (MQ=255)

                                                                                                      tAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggc               <  1:569496/139‑1 (MQ=255)

                                                                                                        aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg             >  2:736995/1‑139 (MQ=255)

                                                                                                        aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg             >  2:354169/1‑139 (MQ=255)

                                                                                                        aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg             >  1:44605/1‑139 (MQ=255)

                                                                                                            gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  1:218060/1‑139 (MQ=255)

                                                                                                            gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  2:125736/1‑139 (MQ=255)

                                                                                                            gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  1:602579/1‑139 (MQ=255)

                                                                                                            gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  1:278026/1‑139 (MQ=255)

                                                                                                               cAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATaa      >  1:2885/1‑139 (MQ=255)

                                                                                                                   ttGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGc  <  2:572443/139‑1 (MQ=255)

TCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGC  >  NC_000913/1411866‑1412119

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