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 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	577,085	G→A	intergenic (‑260/‑313)	nmpC ← / → essD	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	577,085	0	G	A	100.0%	188.9 / NA	48	intergenic (‑260/‑313)	nmpC/essD	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (25/23); total (25/23)

AAGTAGATCTCTATTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGGCTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTGGTTATGCTGTT  >  NC_000913/576940‑577225

aaGTAGATCTCTATTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTaaa                                                                                                                                         <  2:544959/151‑1 (MQ=255)

    aGATCTCTATTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAAt                                                                                                                                      <  1:80394/150‑1 (MQ=255)

        ctctATTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAacac                                                                                                                                 >  1:169632/1‑151 (MQ=255)

          ctATTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATaa                                                                                                                                    <  1:308927/146‑1 (MQ=255)

            aTTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACt                                                                                                                                <  1:155820/148‑1 (MQ=255)

            aTTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTgg                                                                                                                              >  1:275132/1‑150 (MQ=255)

              ttttATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGaa                                                                                                                            >  2:228927/1‑150 (MQ=255)

                       aaCTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTAtttttt                                                                                                                  >  1:225371/1‑151 (MQ=255)

                           tttttCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTgg                                                                                                                <  1:300785/149‑1 (MQ=255)

                           tttttCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGt                                                                                                               <  1:92857/150‑1 (MQ=255)

                                    cGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATttgttg                                                                                                      >  1:542975/1‑150 (MQ=255)

                                         ccTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGAttt                                                                                                <  1:288463/151‑1 (MQ=255)

                                         ccTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGAttt                                                                                                >  2:417526/1‑151 (MQ=255)

                                           tATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTga                                                                                                     <  1:192186/144‑1 (MQ=255)

                                           tATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTga                                                                                                     >  2:192181/1‑144 (MQ=255)

                                               cATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTAt                                                                                          <  2:282312/151‑1 (MQ=255)

                                                      ctTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTAtt                                                                                     <  1:91905/149‑1 (MQ=255)

                                                        tGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGt                                                                                  <  1:369089/150‑1 (MQ=255)

                                                         ggCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAg                                                                                <  2:588004/151‑1 (MQ=255)

                                                          gCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAgt                                                                               >  2:105696/1‑151 (MQ=255)

                                                              aataaaaataaaTCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAgtggtg                                                                           >  2:602308/1‑151 (MQ=255)

                                                              aataaaaataaaTCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAgtggtg                                                                           >  2:184794/1‑151 (MQ=255)

                                                                  aaaataaaTCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGtttt                                                                       >  2:94816/1‑151 (MQ=255)

                                                                           cTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCg                                                              >  1:568660/1‑151 (MQ=255)

                                                                           cTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCg                                                              >  1:486036/1‑151 (MQ=255)

                                                                            tATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCgg                                                             >  1:211687/1‑151 (MQ=255)

                                                                                  ccAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCAt                                                       >  2:190516/1‑151 (MQ=255)

                                                                                         atatTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCa                                                <  1:470127/151‑1 (MQ=255)

                                                                                          tatTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCa                                                >  1:481805/1‑150 (MQ=255)

                                                                                             tAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAat                                             <  1:325218/150‑1 (MQ=255)

                                                                                                cGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCa                                         <  1:503270/151‑1 (MQ=255)

                                                                                                   cTGTTATTTATAAGCGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCAttt                                      >  2:314219/1‑151 (MQ=255)

                                                                                                     gTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTa                                     <  2:212854/150‑1 (MQ=255)

                                                                                                     gTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAg                                    <  1:417533/151‑1 (MQ=255)

                                                                                                      ttatttatAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGt                                   >  1:225873/1‑151 (MQ=255)

                                                                                                        atttatAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTgg                                 >  2:527929/1‑151 (MQ=255)

                                                                                                        atttatAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTg                                  <  2:332887/150‑1 (MQ=255)

                                                                                                         tttatAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGt                                >  2:131138/1‑151 (MQ=255)

                                                                                                                  gCTCTATAATTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTtacgtacg                       <  2:344509/151‑1 (MQ=255)

                                                                                                                         aaTTTGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTaaaaa                 >  2:460897/1‑150 (MQ=255)

                                                                                                                           tttGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAAtt              >  2:558089/1‑151 (MQ=255)

                                                                                                                            ttGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAAtt              <  2:536313/150‑1 (MQ=255)

                                                                                                                             tGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTgg            >  2:450978/1‑151 (MQ=255)

                                                                                                                             tGAAGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTgg            >  2:243660/1‑151 (MQ=255)

                                                                                                                                aGGTTCAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGGTTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTGGTTa         <  1:35236/151‑1 (MQ=255)

                                                                                                                                     cAATTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTGGTTATGCTg    <  2:569505/151‑1 (MQ=255)

                                                                                                                                      aaTTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTGGTTATGCTGt   <  2:498889/151‑1 (MQ=255)

                                                                                                                                       aTTTAAACCGACTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTGGTTATGCTGtt  >  1:84333/1‑151 (MQ=255)

AAGTAGATCTCTATTTTTATCTGAACTTTTTTCTATCGAATCCTATTCATGGCTCTTGGCTGAATAAAAATAAATCTATTAGCCAATTTATATTAACGGCTGTTATTTATAAGTGCTCTATAATTTGAAGGTTCAATTTAAACCGGCTAAAAATAACACTGGAAATTATTTTTTGGTTATTTGTTGAGATTTGCTTATGTATTTGTAGTGGTGTTTTCAATACTCGGTAGCATTCTCTCAAATATCATTTAGTGGTTTACGTACGTAAAAAATTGGTTATGCTGTT  >  NC_000913/576940‑577225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A