BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124978.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,824,732 number of mapped reads = 5,703,252 (97.91%) number of supplementary alignments = 53,212 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,858,139 number of mapped paired reads (second in pair) = 2,845,113 number of mapped paired reads (both in pair) = 5,674,300 number of mapped paired reads (singletons) = 28,952 number of mapped bases = 487,817,232 bp number of sequenced bases = 487,521,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 694,595 duplication rate = 8.42% >>>>>>> Insert size mean insert size = 88,094.4101 std insert size = 2,779,352.0137 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.4137 >>>>>>> ACTG content number of A's = 139,175,802 bp (28.55%) number of C's = 89,966,625 bp (18.45%) number of T's = 146,889,236 bp (30.13%) number of G's = 111,485,057 bp (22.87%) number of N's = 5,109 bp (0%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 3,708,265 number of insertions = 78,872 mapped reads with insertion percentage = 1.34% number of deletions = 159,555 mapped reads with deletion percentage = 2.73% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.1576X std coverageData = 1.9025X There is a 10.05% of reference with a coverageData >= 1X There is a 3.08% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 39583649 0.1588106334146305 1.4263585850092146 chr2 243199373 42460967 0.17459324206399168 2.1633626196690168 chr3 198022430 36782819 0.18575077075864588 0.648521283842874 chr4 191154276 27099668 0.1417685681276625 1.8449669295684303 chr5 180915260 24440963 0.1350961936544214 0.5351897009925205 chr6 171115067 29762960 0.17393535544125988 0.9942749401743493 chr7 159138663 32841182 0.2063683418026454 1.6732239669092481 chr8 146364022 31345734 0.21416283572748498 0.8196597656763783 chr9 141213431 23386916 0.16561396344799525 1.8659412684603722 chr10 135534747 28624340 0.21119558366829724 6.160904217694775 chr11 135006516 18872169 0.13978709738721057 0.8434551385717841 chr12 133851895 24581458 0.18364669398218084 0.6130298761574319 chr13 115169878 11920626 0.10350472021859744 0.4348248424942112 chr14 107349540 11964322 0.11145200994806312 0.5598841000278647 chr15 102531392 11828435 0.11536403407065808 0.48249199134235216 chr16 90354753 17480387 0.19346394538868364 3.2393668251394656 chr17 81195210 10872809 0.13390948801043806 1.4073270304219305 chr18 78077248 9488727 0.12152998783973533 1.895605270920099 chr19 59128983 7522587 0.12722334493728735 0.8508293818843196 chr20 63025520 8429860 0.13375312095798655 0.720401503515999 chr21 48129895 5171733 0.10745365224669616 0.9616056746001364 chr22 51304566 4208850 0.08203655791572236 0.45528851396103115 chrMT 16571 241396 14.567376742501962 9.385413735414662 chrX 155270560 20694643 0.1332811770627993 0.6945515564487946 chrY 59373566 8210032 0.13827756277936884 3.16858236492075