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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,494,973	G→A	92 (TAG→TAA)	ypdI →	putative lipoprotein involved in colanic acid biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,494,973	0	G	A	97.1%	208.7 / ‑1.9	68	92 (TAG→TAA)	ypdI	putative lipoprotein involved in colanic acid biosynthesis
Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (35/31); total (36/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

TCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATTATCTTATTCATCCTGTGCGATAGCGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCACTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCAAG  >  NC_000913/2494842‑2495106

tctACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCttt                                                                                                                                >  2:75632/1‑139 (MQ=255)

  tACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTca                                                                                                                              >  1:1052387/1‑139 (MQ=255)

    cAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTcaca                                                                                                                            >  1:528293/1‑139 (MQ=255)

        aCTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGc                                                                                                                        <  2:824133/139‑1 (MQ=255)

          ttCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                                                                      >  2:911525/1‑139 (MQ=255)

          ttCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                                                                      >  1:768150/1‑139 (MQ=255)

          ttCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                                                                      >  1:399023/1‑139 (MQ=255)

            cAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGt                                                                                                                    >  1:76282/1‑139 (MQ=255)

                 aTCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATTATCTTATTCATCCTGTGCGATAGCGTCTTTCACATGGCAGGt                                                                                                                    >  2:159757/1‑134 (MQ=255)

                 aTCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATTATCTTATTCATCCTGTGCGATAGCGTCTTTCACATGGCAGGt                                                                                                                    <  1:159757/134‑1 (MQ=255)

                         cGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTc                                                                                                       <  2:768150/139‑1 (MQ=255)

                             tttGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgat                                                                                                   >  1:99199/1‑139 (MQ=255)

                              ttGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatg                                                                                                  <  1:55990/139‑1 (MQ=255)

                                gTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgct                                                                                                <  2:99199/139‑1 (MQ=255)

                                 tttAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgctg                                                                                               <  2:76282/139‑1 (MQ=255)

                                         gagagaAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACAt                                                                                                                           <  2:958842/103‑1 (MQ=255)

                                         gagagaAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACAt                                                                                                                           >  1:958842/1‑103 (MQ=255)

                                               agaTGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGc                                                                                 <  2:173860/139‑1 (MQ=255)

                                                    cgcCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACAt                                                                                                                           <  2:114109/92‑1 (MQ=255)

                                                    cgcCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACAt                                                                                                                           >  1:114109/1‑92 (MQ=255)

                                                      ccaccaTTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATg                                                                          >  1:1286949/1‑139 (MQ=255)

                                                      ccaccaTTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATg                                                                          >  2:79991/1‑139 (MQ=255)

                                                        accaTTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                                                                        <  1:767654/139‑1 (MQ=255)

                                                        accaTTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                                                                        <  1:911525/139‑1 (MQ=255)

                                                              aaaCCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATcc                                                                  <  2:528293/139‑1 (MQ=255)

                                                                    cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGAccc                                                            >  1:1259597/1‑139 (MQ=255)

                                                                         aagaaATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTc                                                                                                                                   >  2:886582/1‑63 (MQ=255)

                                                                         aagaaATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTc                                                                                                                                   <  1:886582/63‑1 (MQ=255)

                                                                         aagaaATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCaa                                                                             <  2:169271/117‑1 (MQ=255)

                                                                         aagaaATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCaa                                                                             >  1:169271/1‑117 (MQ=255)

                                                                           gaaATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGTGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCg                                                     >  2:1155248/1‑139 (MQ=255)

                                                                            aaaTGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGc                                                    <  1:75632/139‑1 (MQ=255)

                                                                            aaaTGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGc                                                    <  1:547584/139‑1 (MQ=255)

                                                                            aaaTGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGc                                                    <  2:1286949/139‑1 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGc                                                                                                                        <  1:1152754/64‑1 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGc                                                                                                                        >  2:1152754/1‑64 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGa                                                                                                                  >  1:508371/1‑70 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGa                                                                                                                  <  2:508371/70‑1 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgct                                                                                                <  2:511562/88‑1 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgct                                                                                                >  1:511562/1‑88 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGAtgtg                                                                                          >  1:1139525/1‑94 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGAtgtg                                                                                          <  2:1139525/94‑1 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGAc                                                              <  1:836594/122‑1 (MQ=255)

                                                                                   gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGAc                                                              >  2:836594/1‑122 (MQ=255)

                                                                                    cccccTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATa                                            <  1:1011359/139‑1 (MQ=255)

                                                                                    cccccTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATa                                            >  2:1011359/1‑139 (MQ=255)

                                                                                    cccccTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATa                                            >  2:1236086/1‑139 (MQ=255)

                                                                                          tttCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGaa                                                                                                                 <  1:1266385/64‑1 (MQ=255)

                                                                                          tttCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGaa                                                                                                                 >  2:1266385/1‑64 (MQ=255)

                                                                                                                ttATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCca                <  2:2032/139‑1 (MQ=255)

                                                                                                                ttATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCca                <  1:93849/139‑1 (MQ=255)

                                                                                                                  aTTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                                                                        >  2:613797/1‑81 (MQ=255)

                                                                                                                  aTTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                                                                        <  1:613797/81‑1 (MQ=255)

                                                                                                                   ttCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAac                                                                                       <  2:815399/65‑1 (MQ=255)

                                                                                                                   ttCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAac                                                                                       >  1:815399/1‑65 (MQ=255)

                                                                                                                        ccTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATa                                            >  2:919599/1‑103 (MQ=255)

                                                                                                                        ccTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATa                                            <  1:919599/103‑1 (MQ=255)

                                                                                                                        ccTGTACGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCgg        >  2:271844/1‑139 (MQ=255)

                                                                                                                          tgtgCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCgggg      >  1:290416/1‑139 (MQ=255)

                                                                                                                            tgCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACCCCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCa    >  2:88432/1‑139 (MQ=255)

                                                                                                                            tgCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCa    >  1:268138/1‑139 (MQ=255)

                                                                                                                            tgCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCa    >  1:282920/1‑139 (MQ=255)

                                                                                                                             gCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGcc                                               <  1:668655/95‑1 (MQ=255)

                                                                                                                             gCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGcc                                               >  2:668655/1‑95 (MQ=255)

                                                                                                                             gCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCaa   <  2:282920/139‑1 (MQ=255)

                                                                                                                             gCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCaa   <  2:1052387/139‑1 (MQ=255)

                                                                                                                             gCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCaa   >  2:501167/1‑139 (MQ=255)

                                                                                                                              cGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGTGCAAg  >  1:714845/1‑139 (MQ=255)

TCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATTATCTTATTCATCCTGTGCGATAGCGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCACTACCGCCTGCCATACCCCACCATAAAGCGAATCATCAAGCCACAAGCCGGGGCAAG  >  NC_000913/2494842‑2495106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A