BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630583.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 33,191,046 number of mapped reads = 32,640,795 (98.34%) number of supplementary alignments = 83,144 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,414,894 number of mapped paired reads (second in pair) = 16,225,901 number of mapped paired reads (both in pair) = 32,373,410 number of mapped paired reads (singletons) = 267,385 number of mapped bases = 3,168,907,699 bp number of sequenced bases = 3,166,585,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,670,297 duplication rate = 8.87% >>>>>>> Insert size mean insert size = 44,713.893 std insert size = 2,150,087.0521 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 54.0143 >>>>>>> ACTG content number of A's = 933,733,334 bp (29.49%) number of C's = 623,282,461 bp (19.68%) number of T's = 943,487,570 bp (29.8%) number of G's = 665,606,449 bp (21.02%) number of N's = 475,648 bp (0.02%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 27,857,627 number of insertions = 590,736 mapped reads with insertion percentage = 1.77% number of deletions = 1,684,599 mapped reads with deletion percentage = 5.02% homopolymer indels = 54% >>>>>>> Coverage mean coverageData = 1.0237X std coverageData = 5.2288X There is a 19.66% of reference with a coverageData >= 1X There is a 13.45% of reference with a coverageData >= 2X There is a 9.96% of reference with a coverageData >= 3X There is a 7.81% of reference with a coverageData >= 4X There is a 6.32% of reference with a coverageData >= 5X There is a 5.22% of reference with a coverageData >= 6X There is a 4.39% of reference with a coverageData >= 7X There is a 3.74% of reference with a coverageData >= 8X There is a 3.21% of reference with a coverageData >= 9X There is a 2.79% of reference with a coverageData >= 10X There is a 2.43% of reference with a coverageData >= 11X There is a 2.13% of reference with a coverageData >= 12X There is a 1.88% of reference with a coverageData >= 13X There is a 1.67% of reference with a coverageData >= 14X There is a 1.48% of reference with a coverageData >= 15X There is a 1.32% of reference with a coverageData >= 16X There is a 1.19% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 0.96% of reference with a coverageData >= 19X There is a 0.86% of reference with a coverageData >= 20X There is a 0.78% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.64% of reference with a coverageData >= 23X There is a 0.58% of reference with a coverageData >= 24X There is a 0.53% of reference with a coverageData >= 25X There is a 0.49% of reference with a coverageData >= 26X There is a 0.44% of reference with a coverageData >= 27X There is a 0.41% of reference with a coverageData >= 28X There is a 0.37% of reference with a coverageData >= 29X There is a 0.34% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 264845081 1.0625653807297837 7.3741781768589005 chr2 243199373 276903163 1.1385850201184524 7.896950551391191 chr3 198022430 220634237 1.1141881099024995 4.013886046669005 chr4 191154276 194145758 1.0156495688330822 4.508078041347995 chr5 180915260 197937554 1.094089873900079 3.9178208770009677 chr6 171115067 187351215 1.094884385604688 4.456293598385552 chr7 159138663 159844120 1.0044329705094983 4.048614680976928 chr8 146364022 156190587 1.0671378448455044 3.9941586783921994 chr9 141213431 133240913 0.9435427781653433 5.989522244970353 chr10 135534747 146445877 1.0805043004949868 4.540576496895761 chr11 135006516 154384314 1.1435323166179623 6.203704121110429 chr12 133851895 140043203 1.0462549148071456 3.89382132817557 chr13 115169878 94902536 0.8240221978875414 3.356131246336043 chr14 107349540 97216360 0.905605743629642 3.7698291855767376 chr15 102531392 95429226 0.9307317899282983 3.743834564606766 chr16 90354753 92135504 1.01970843747423 7.732103275079663 chr17 81195210 79766425 0.9824030875712988 4.061763696466072 chr18 78077248 84340480 1.0802184011403682 6.588098014285137 chr19 59128983 47726199 0.8071540652069054 4.504083115125691 chr20 63025520 75454440 1.1972045609461057 4.4709467161204675 chr21 48129895 41467481 0.86157430844177 4.72451310755741 chr22 51304566 34869275 0.6796524699185643 3.4230862278206144 chrMT 16571 4491 0.27101562971456156 1.0435265843047752 chrX 155270560 187871124 1.2099597244963887 4.544607430130901 chrY 59373566 5758136 0.09698147488732613 3.717560854579596