BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038433.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 = 16,440,166 number of mapped reads = 15,576,850 (94.75%) number of supplementary alignments = 240,782 (1.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,911,956 number of mapped paired reads (second in pair) = 7,664,894 number of mapped paired reads (both in pair) = 15,283,158 number of mapped paired reads (singletons) = 293,692 number of mapped bases = 2,104,702,401 bp number of sequenced bases = 2,103,244,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,657,166 duplication rate = 11.77% >>>>>>> Insert size mean insert size = 92,491.8899 std insert size = 2,964,302.5119 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 53.3948 >>>>>>> ACTG content number of A's = 601,348,825 bp (28.59%) number of C's = 417,101,132 bp (19.83%) number of T's = 614,110,021 bp (29.2%) number of G's = 470,519,417 bp (22.37%) number of N's = 164,696 bp (0.01%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 27,711,837 number of insertions = 364,846 mapped reads with insertion percentage = 2.22% number of deletions = 746,092 mapped reads with deletion percentage = 4.61% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.6799X std coverageData = 9.5644X There is a 29.79% of reference with a coverageData >= 1X There is a 15.54% of reference with a coverageData >= 2X There is a 7.94% of reference with a coverageData >= 3X There is a 4.44% of reference with a coverageData >= 4X There is a 2.47% of reference with a coverageData >= 5X There is a 1.44% of reference with a coverageData >= 6X There is a 0.85% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 187853773 0.7536742426009844 13.49253339008799 chr2 243199373 192446639 0.7913122333584306 10.316230164383478 chr3 198022430 146874837 0.7417080832711729 1.5855477586715403 chr4 191154276 90570670 0.4738092806252474 8.080443464183897 chr5 180915260 147450508 0.8150252665253335 1.5566010480924093 chr6 171115067 123885060 0.7239868596726202 7.538903980673532 chr7 159138663 103648436 0.6513089531234783 10.166277838974517 chr8 146364022 136242582 0.9308474865496659 3.647503656465488 chr9 141213431 91469592 0.6477400297709642 15.327506383658633 chr10 135534747 116930457 0.8627341666119022 25.887734115824554 chr11 135006516 98019009 0.7260316902037528 7.684665070162455 chr12 133851895 87844225 0.6562792779287884 1.5295248037216052 chr13 115169878 71333433 0.619375779837155 1.304869926974058 chr14 107349540 69863421 0.650803170651686 1.4383203443524968 chr15 102531392 58601862 0.5715504379380707 1.2759399553732402 chr16 90354753 69569977 0.7699647742936113 10.266825681290486 chr17 81195210 53227644 0.6555515282243867 11.612431718722021 chr18 78077248 63638375 0.8150693912777254 10.540415094655273 chr19 59128983 28791544 0.4869277727979864 5.592708294385676 chr20 63025520 57642731 0.9145935011722236 2.935654333652156 chr21 48129895 18019413 0.3743912800973283 3.7917319057668233 chr22 51304566 12031931 0.2345196916781247 0.8141052848732115 chrMT 16571 3195404 192.831090459236 97.96473182055213 chrX 155270560 71111097 0.45798184150298676 2.1138786105022227 chrY 59373566 4439781 0.07477706493155557 7.8949542084427655