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 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,106,320	G→A	167 (TAG→TAA)	cpxP →	inhibitor of the cpx response, periplasmic adaptor protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,106,320	0	G	A	98.2%	169.8 / ‑4.2	55	167 (TAG→TAA)	cpxP	inhibitor of the cpx response, periplasmic adaptor protein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (25/29); total (25/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

CGCCTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAGCGTCAGTTGA  >  NC_000913/4106183‑4106454

cGCCTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCagtagt                                                                                                                                       >  2:303361/1‑139 (MQ=255)

  ccTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGtaataa                                                                                                                                     >  2:1048781/1‑139 (MQ=255)

  ccTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGtaataa                                                                                                                                     >  2:531749/1‑139 (MQ=255)

              ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                                         <  1:32453/139‑1 (MQ=255)

              ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                                         <  1:531749/139‑1 (MQ=255)

              ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                                         <  1:1048781/139‑1 (MQ=255)

               gAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCt                                                                                                                        >  1:1103266/1‑139 (MQ=255)

                agcagcAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCtt                                                                                                                       >  1:979986/1‑139 (MQ=255)

                 gcagcaAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTg                                                                                                                      <  1:1399773/139‑1 (MQ=255)

                       aGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATa                                                                                                                 <  2:802044/138‑1 (MQ=255)

                       aGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATa                                                                                                                 >  1:802044/1‑138 (MQ=255)

                                aaaCGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATcc                                                                                                       <  1:337044/139‑1 (MQ=255)

                                      gaAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCt                                                                                                 >  1:1158950/1‑139 (MQ=255)

                                            tCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTccccc                                                                                           <  2:606445/139‑1 (MQ=255)

                                            tCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTccccc                                                                                           >  2:1280775/1‑139 (MQ=255)

                                              aacaacGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACGCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcac                                                                                         >  1:352153/1‑139 (MQ=255)

                                               acaacGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                                        <  1:572247/139‑1 (MQ=255)

                                                caacGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACAt                                                                                       >  1:1063212/1‑139 (MQ=255)

                                                  acGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCAt                                                                                                         >  1:1234320/1‑119 (MQ=255)

                                                  acGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCAt                                                                                                         <  2:1234320/119‑1 (MQ=255)

                                                    gAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACGCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCtg                                                                                   <  2:352153/139‑1 (MQ=255)

                                                    gAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCtg                                                                                   >  2:365275/1‑139 (MQ=255)

                                                     aaTGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCtgt                                                                                  >  2:917210/1‑139 (MQ=255)

                                                     aaTGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCtgt                                                                                  >  2:1246422/1‑139 (MQ=255)

                                                       tGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                <  2:744946/123‑1 (MQ=255)

                                                       tGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                >  1:744946/1‑123 (MQ=255)

                                                            cAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGtt                                                                           >  1:1424229/1‑139 (MQ=255)

                                                               ttGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGttttt                                                                        >  2:525420/1‑139 (MQ=255)

                                                                         tgacgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCa                                                              >  2:98924/1‑139 (MQ=255)

                                                                             gCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAAttt                                                          <  1:303361/139‑1 (MQ=255)

                                                                                 tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCAt                                                                                                                  >  1:692238/1‑79 (MQ=255)

                                                                                 tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCAt                                                                                                                  <  2:692238/79‑1 (MQ=255)

                                                                                 tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCCTCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCct                                                      >  1:1600178/1‑139 (MQ=255)

                                                                                 tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCct                                                      >  2:1105532/1‑139 (MQ=255)

                                                                                  ggCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCctg                                                     <  1:1105532/139‑1 (MQ=255)

                                                                                  ggCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCctg                                                     <  1:1341913/139‑1 (MQ=255)

                                                                                  ggCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCctg                                                     <  2:1424229/139‑1 (MQ=255)

                                                                                  ggCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCctg                                                     <  1:1246422/139‑1 (MQ=255)

                                                                                    cAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCt                                                                                                                        >  1:459101/1‑70 (MQ=255)

                                                                                    cAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCt                                                                                                                        <  2:459101/70‑1 (MQ=255)

                                                                                             tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                                        >  2:1329602/1‑93 (MQ=255)

                                                                                             tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                                        <  1:1329602/93‑1 (MQ=255)

                                                                                              cATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCGGTAATAAACCCTGTTTTCCTTGCCATCGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCa                                         <  2:979986/139‑1 (MQ=255)

                                                                                              cATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCa                                         <  1:525420/139‑1 (MQ=255)

                                                                                                     gAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                >  2:312202/1‑77 (MQ=255)

                                                                                                     gAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                <  1:312202/77‑1 (MQ=255)

                                                                                                             tGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc                          <  2:634562/139‑1 (MQ=255)

                                                                                                              gAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         <  2:1158950/139‑1 (MQ=255)

                                                                                                                gtagtaGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTc                       <  1:51262/139‑1 (MQ=255)

                                                                                                                  agtagCAACTCACGTTCCCAGTAATAATCCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCg                     <  1:365275/139‑1 (MQ=255)

                                                                                                                  agtagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCg                     <  2:1063212/139‑1 (MQ=255)

                                                                                                                      gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc                          >  1:1166993/1‑130 (MQ=255)

                                                                                                                      gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc                          <  2:1166993/130‑1 (MQ=255)

                                                                                                                      gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTtat                 >  2:1465219/1‑139 (MQ=255)

                                                                                                                             aCGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGcc                                                       <  1:1280268/94‑1 (MQ=255)

                                                                                                                             aCGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGcc                                                       >  2:1280268/1‑94 (MQ=255)

                                                                                                                               gTTCCCAGTAATGAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         <  2:1529886/122‑1 (MQ=255)

                                                                                                                               gTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         >  1:1529886/1‑122 (MQ=255)

                                                                                                                                     agtaatAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAGCGTCAGTTGa  >  2:630962/1‑139 (MQ=255)

CGCCTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAGCGTCAGTTGA  >  NC_000913/4106183‑4106454

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A