BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038476.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 20,376,334 number of mapped reads = 18,306,452 (89.84%) number of supplementary alignments = 329,820 (1.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,282,077 number of mapped paired reads (second in pair) = 9,024,375 number of mapped paired reads (both in pair) = 17,980,078 number of mapped paired reads (singletons) = 326,374 number of mapped bases = 2,425,514,907 bp number of sequenced bases = 2,423,741,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,416,686 duplication rate = 17.13% >>>>>>> Insert size mean insert size = 88,041.5008 std insert size = 2,877,376.5849 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 53.3207 >>>>>>> ACTG content number of A's = 686,957,362 bp (28.34%) number of C's = 489,811,364 bp (20.21%) number of T's = 696,179,446 bp (28.72%) number of G's = 550,607,188 bp (22.72%) number of N's = 186,631 bp (0.01%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 31,857,912 number of insertions = 445,209 mapped reads with insertion percentage = 2.3% number of deletions = 874,791 mapped reads with deletion percentage = 4.6% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.7835X std coverageData = 12.7022X There is a 28.06% of reference with a coverageData >= 1X There is a 16.97% of reference with a coverageData >= 2X There is a 9.71% of reference with a coverageData >= 3X There is a 6.24% of reference with a coverageData >= 4X There is a 3.88% of reference with a coverageData >= 5X There is a 2.55% of reference with a coverageData >= 6X There is a 1.67% of reference with a coverageData >= 7X There is a 1.13% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193181110 0.7750476577548828 17.80041669034651 chr2 243199373 213390303 0.8774294948531796 11.74504409162889 chr3 198022430 158502543 0.8004272192801594 2.0445025456346904 chr4 191154276 157367118 0.8232466533994772 11.493428498766908 chr5 180915260 141919939 0.7844553245536059 1.7530948435807276 chr6 171115067 136827402 0.7996221747089051 7.521955178877948 chr7 159138663 125623730 0.7893979227411254 10.808564186144439 chr8 146364022 121828685 0.8323677044075763 3.6400777704722156 chr9 141213431 100549427 0.7120386941097692 17.009195842710383 chr10 135534747 143917790 1.0618516150696027 38.71560481398694 chr11 135006516 111479993 0.8257378703113856 7.28377358027328 chr12 133851895 102286260 0.764174911382465 1.873998672290683 chr13 115169878 70555815 0.6126238581237361 1.5246969377314825 chr14 107349540 69219274 0.6448027071191921 1.8053549816847163 chr15 102531392 66439609 0.6479928508139244 1.609391267666672 chr16 90354753 87695416 0.9705678239195673 17.03133020595169 chr17 81195210 62934663 0.7751031495577141 13.169766551337085 chr18 78077248 67192354 0.8605881447051003 14.577082728994222 chr19 59128983 35805272 0.605545202764607 8.312025653672023 chr20 63025520 51547380 0.8178810742061311 3.709578643592573 chr21 48129895 30588253 0.6355354193064414 5.833746674115981 chr22 51304566 25487226 0.4967828009694108 1.5155695396624684 chrMT 16571 4301566 259.58397199927583 172.40885693526639 chrX 155270560 137613720 0.8862834010516868 3.7531222518154532 chrY 59373566 9260059 0.1559626551654317 13.071444208097972