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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,207,942	(G)_7→8	coding (442/630 nt)	stfP →	e14 prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,207,935	1	.	G	95.8%	164.2 / ‑0.9	48	coding (435/630 nt)	stfP	e14 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand): ref base . (2/0); new base G (27/19); total (29/19)
Fisher's exact test for biased strand distribution p-value = 5.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑G‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGT  >  NC_000913/1207799‑1208065

GAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑g                                                                                                                                  <  1:426825‑M1/139‑1 (MQ=255)

 AGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gg                                                                                                                                 >  2:698453‑M1/1‑139 (MQ=255)

        gCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggggat                                                                                                                          <  2:653308/139‑4 (MQ=255)

               tCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATa                                                                                                                    <  2:218454/139‑1 (MQ=255)

                    gcagcaACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGtt                                                                                                               <  2:39033/139‑1 (MQ=255)

                      agccACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGCGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             >  2:38167/1‑122 (MQ=255)

                      agcaACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGt                                                                                                             >  2:474264/1‑139 (MQ=255)

                      agcaACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             <  1:38167/122‑1 (MQ=255)

                        caACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGACTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTAt                                                                                                           >  2:666549/1‑139 (MQ=255)

                                    tAGGACGCACCGATTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATAGAAATACAGTTGTATTCCCGGTTGCGt                                                                                               <  2:459869/139‑1 (MQ=255)

                                       gACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             <  2:376671/105‑1 (MQ=255)

                                       gACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             >  1:376671/1‑105 (MQ=255)

                                        aCGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑GAGGGGGGATGGAAATAAAGTTGTATTCCCGGTTGCGTTtaa                                                                                           >  1:104849/1‑139 (MQ=255)

                                           cACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTtaataa                                                                                        >  2:93816/1‑139 (MQ=255)

                                            aCCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTaataat                                                                                       >  1:623311/1‑139 (MQ=255)

                                                               cGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTTGGATTGGAATTCCGCTAAAACACCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGAAGTCTCGGTTTCGTTTAATAATGTCTGTGTTGCCGttgttg                                                                    <  2:104849/139‑1 (MQ=255)

                                                                 gctATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGttgttg                                                                    >  2:644505/3‑137 (MQ=255)

                                                                 gctATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGttgttg                                                                    <  1:644505/135‑1 (MQ=255)

                                                                   tATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGttgttg                                                                    >  2:281584/1‑135 (MQ=255)

                                                                   tATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGttgttg                                                                    <  1:281584/135‑1 (MQ=255)

                                                                      gATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTa                                                             >  2:53637/1‑139 (MQ=255)

                                                                         tggtggTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGa                                                          >  2:562045/1‑139 (MQ=255)

                                                                            tggtATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACaa                                                       <  2:426825/139‑1 (MQ=255)

                                                                            tggtATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACaa                                                       <  1:3267/139‑1 (MQ=255)

                                                                              gtATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑g                                                                                                                                  >  1:105837/1‑61 (MQ=255)

                                                                              gtATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑g                                                                                                                                  <  2:105837/61‑1 (MQ=255)

                                                                                     gCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAgcgc                                              >  1:411180/1‑139 (MQ=255)

                                                                                      cAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑ggg                                                                                                                                >  2:176424/1‑55 (MQ=255)

                                                                                      cAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑ggg                                                                                                                                <  1:176424/55‑1 (MQ=255)

                                                                                        aTCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCAcc                                           >  1:93931/1‑139 (MQ=255)

                                                                                         tCAGTAATCATTCAGTTGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCa                                                                  <  2:150188/115‑1 (MQ=255)

                                                                                         tCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCa                                                                  >  1:150188/1‑115 (MQ=255)

                                                                                         tCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCt                                          >  2:85883/1‑139 (MQ=255)

                                                                                         tCAGTAATCAGTCAGAGGGGGTGGAATGTCGCAAAAGCACCTGCCTCGG‑G‑GGGGGGATGGAAATACAGGGTTATTCCCGGTTGCGTTTAGTAATGCCTGGGTTGCCATTGATGCAATTTATGACAATTTTACCGCActt                                          >  2:630588/1‑137 (MQ=255)

                                                                                           ggTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTAt                                        >  2:481694/2‑139 (MQ=255)

                                                                                              aaTCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             <  2:95482/50‑1 (MQ=255)

                                                                                              aaTCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             >  1:95482/1‑50 (MQ=255)

                                                                                                   ttCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCgg                                                                                                     <  1:121070/70‑1 (MQ=255)

                                                                                                   ttCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCgg                                                                                                     >  2:121070/1‑70 (MQ=255)

                                                                                                   ttCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAg                                >  1:104034/1‑139 (MQ=255)

                                                                                                   ttCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             >  2:544373/1‑45 (MQ=255)

                                                                                                   ttCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑g‑gggggg                                                                                                                             <  1:544373/45‑1 (MQ=255)

                                                                                                     cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTg                              >  2:32340/1‑139 (MQ=255)

                                                                                                     cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTg                              >  2:521160/1‑139 (MQ=255)

                                                                                                        tGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGTGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCa                           >  1:479568/1‑139 (MQ=255)

                                                                                                          ggggTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAAc                         <  1:93816/139‑1 (MQ=255)

                                                                                                          ggggTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAAc                         >  2:448595/1‑139 (MQ=255)

                                                                                                           gggTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACg                        <  1:303576/139‑1 (MQ=255)

                                                                                                             gTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTtaat                                                                                          <  2:279625/71‑1 (MQ=255)

                                                                                                             gTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTtaat                                                                                          >  1:279625/1‑71 (MQ=255)

                                                                                                             gTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACggg                      <  1:562045/139‑1 (MQ=255)

                                                                                                             gTGGAATGCCGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACggg                      >  2:385761/1‑139 (MQ=255)

                                                                                                                     ccGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGaaa                                                                                                                      <  2:478065/35‑1 (MQ=255)

                                                                                                                     ccGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGaaa                                                                                                                      >  1:478065/1‑35 (MQ=255)

                                                                                                                     ccGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAgc                                                <  1:26379/105‑1 (MQ=255)

                                                                                                                     ccGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAgc                                                >  2:26379/1‑105 (MQ=255)

                                                                                                                     ccGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata              >  1:61981/1‑139 (MQ=255)

                                                                                                                      cGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCaaa                                                                <  1:455705/88‑1 (MQ=255)

                                                                                                                      cGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATAc             >  1:405736/1‑139 (MQ=255)

                                                                                                                      cGCAAAAGCATCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGATGCaaa                                                                >  2:455705/1‑88 (MQ=255)

                                                                                                                                tCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGc                            <  1:132727/114‑1 (MQ=255)

                                                                                                                                tCTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGc                            >  2:132727/1‑114 (MQ=255)

                                                                                                                                 cTGCCTC‑TGG‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGt  <  1:474264/139‑1 (MQ=255)

GAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTC‑T‑G‑GGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGT  >  NC_000913/1207799‑1208065

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