BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975273.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 64,890,198 number of mapped reads = 64,752,123 (99.79%) number of supplementary alignments = 109,429 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 32,390,455 number of mapped paired reads (second in pair) = 32,361,668 number of mapped paired reads (both in pair) = 64,689,702 number of mapped paired reads (singletons) = 62,421 number of mapped bases = 6,020,492,689 bp number of sequenced bases = 6,018,338,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,511,744 duplication rate = 46.5% >>>>>>> Insert size mean insert size = 80,758.9936 std insert size = 2,805,924.8628 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 56.1244 >>>>>>> ACTG content number of A's = 1,610,463,944 bp (26.76%) number of C's = 1,327,979,419 bp (22.07%) number of T's = 1,643,868,674 bp (27.31%) number of G's = 1,435,762,961 bp (23.86%) number of N's = 263,310 bp (0%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 38,560,992 number of insertions = 682,527 mapped reads with insertion percentage = 1.04% number of deletions = 1,520,712 mapped reads with deletion percentage = 2.31% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 1.9448X std coverageData = 26.3035X There is a 12.55% of reference with a coverageData >= 1X There is a 6.31% of reference with a coverageData >= 2X There is a 3.73% of reference with a coverageData >= 3X There is a 2.82% of reference with a coverageData >= 4X There is a 2.29% of reference with a coverageData >= 5X There is a 2.03% of reference with a coverageData >= 6X There is a 1.85% of reference with a coverageData >= 7X There is a 1.73% of reference with a coverageData >= 8X There is a 1.64% of reference with a coverageData >= 9X There is a 1.57% of reference with a coverageData >= 10X There is a 1.51% of reference with a coverageData >= 11X There is a 1.46% of reference with a coverageData >= 12X There is a 1.42% of reference with a coverageData >= 13X There is a 1.38% of reference with a coverageData >= 14X There is a 1.34% of reference with a coverageData >= 15X There is a 1.31% of reference with a coverageData >= 16X There is a 1.28% of reference with a coverageData >= 17X There is a 1.25% of reference with a coverageData >= 18X There is a 1.22% of reference with a coverageData >= 19X There is a 1.19% of reference with a coverageData >= 20X There is a 1.17% of reference with a coverageData >= 21X There is a 1.15% of reference with a coverageData >= 22X There is a 1.12% of reference with a coverageData >= 23X There is a 1.1% of reference with a coverageData >= 24X There is a 1.08% of reference with a coverageData >= 25X There is a 1.06% of reference with a coverageData >= 26X There is a 1.05% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 1.01% of reference with a coverageData >= 29X There is a 1% of reference with a coverageData >= 30X There is a 0.98% of reference with a coverageData >= 31X There is a 0.97% of reference with a coverageData >= 32X There is a 0.95% of reference with a coverageData >= 33X There is a 0.94% of reference with a coverageData >= 34X There is a 0.92% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.9% of reference with a coverageData >= 37X There is a 0.88% of reference with a coverageData >= 38X There is a 0.87% of reference with a coverageData >= 39X There is a 0.86% of reference with a coverageData >= 40X There is a 0.85% of reference with a coverageData >= 41X There is a 0.84% of reference with a coverageData >= 42X There is a 0.83% of reference with a coverageData >= 43X There is a 0.82% of reference with a coverageData >= 44X There is a 0.81% of reference with a coverageData >= 45X There is a 0.8% of reference with a coverageData >= 46X There is a 0.79% of reference with a coverageData >= 47X There is a 0.78% of reference with a coverageData >= 48X There is a 0.77% of reference with a coverageData >= 49X There is a 0.76% of reference with a coverageData >= 50X There is a 0.75% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 732376894 2.9383152228936673 34.776164366891514 chr2 243199373 451849697 1.857939399375014 23.909507382720424 chr3 198022430 415562232 2.0985614205421075 27.838343825687183 chr4 191154276 141375930 0.7395907272301876 12.912166395297119 chr5 180915260 301878461 1.6686180093376313 22.646542540541507 chr6 171115067 540427256 3.158268091026724 41.16019087361173 chr7 159138663 321270526 2.01880875422461 27.560341146125992 chr8 146364022 217957394 1.4891459733184977 20.486657362056626 chr9 141213431 252032889 1.7847657068823715 24.201885471276988 chr10 135534747 276084593 2.037002312034419 25.444972314634438 chr11 135006516 287307927 2.1281041501730185 27.005678613115325 chr12 133851895 341757742 2.553252921820793 29.15706300648712 chr13 115169878 133095369 1.1556439175875484 20.246431468022617 chr14 107349540 206388079 1.9225800036031826 25.69587180548744 chr15 102531392 224359078 2.1881988883950783 27.103698697168838 chr16 90354753 194301748 2.1504319534800787 26.444769437702973 chr17 81195210 228573339 2.8151086621981767 29.29800876174889 chr18 78077248 117953207 1.5107244430541404 22.89347753066232 chr19 59128983 231986927 3.923404652503494 37.65876235991148 chr20 63025520 71965910 1.141853490459103 19.247771249072773 chr21 48129895 61370266 1.2750966109525068 20.629114115871268 chr22 51304566 104539578 2.03762717727697 24.839130126304127 chrMT 16571 169558 10.232212902057812 19.541777817993513 chrX 155270560 153127179 0.9861958313282312 15.740667110121107 chrY 59373566 12780910 0.21526263051136257 5.23988324820152