BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008827.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,750,441 number of mapped reads = 939,733 (34.17%) number of supplementary alignments = 5,331 (0.19%) number of secondary alignments = 0 number of mapped bases = 61,314,661 bp number of sequenced bases = 61,283,005 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,640 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7426 >>>>>>> ACTG content number of A's = 16,440,493 bp (26.83%) number of C's = 11,894,028 bp (19.41%) number of T's = 18,746,308 bp (30.59%) number of G's = 14,116,261 bp (23.03%) number of N's = 85,915 bp (0.14%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 569,850 number of insertions = 4,950 mapped reads with insertion percentage = 0.52% number of deletions = 17,406 mapped reads with deletion percentage = 1.83% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.4064X There is a 1.59% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 7430655 0.029811981892715125 0.9023351673986647 chr2 243199373 5547195 0.022809248772199753 0.3452420158044086 chr3 198022430 5329363 0.026912925975102923 0.2809876113029409 chr4 191154276 3756225 0.01965022744246642 0.197810685298281 chr5 180915260 2693246 0.014886781800495989 0.1442487668053689 chr6 171115067 2659427 0.015541746537141583 0.15239808787128084 chr7 159138663 3210691 0.02017543027868721 0.22052507272254582 chr8 146364022 2131121 0.014560415673737089 0.2973213636240545 chr9 141213431 1963087 0.01390156011434918 0.21071590452000302 chr10 135534747 4009972 0.029586302322901742 1.0577286891289321 chr11 135006516 4001703 0.02964081378116594 0.227336923649652 chr12 133851895 1032407 0.00771305479089407 0.1295269899114382 chr13 115169878 1000948 0.008691057222444917 0.1089164034850435 chr14 107349540 1610329 0.015000800189735326 0.1797336215992295 chr15 102531392 2029875 0.019797595257460273 0.16883150165795013 chr16 90354753 1678802 0.018580118303239676 0.3145839510551156 chr17 81195210 1499690 0.01847017822849402 0.20995233804012617 chr18 78077248 813470 0.010418784227640811 0.3494125788386375 chr19 59128983 1297519 0.02194387479994371 0.49648733827313035 chr20 63025520 1608913 0.0255279607371744 0.19325037906357306 chr21 48129895 797219 0.016563904824641734 0.26139658225716383 chr22 51304566 728443 0.01419840487491893 0.13835989238726798 chrMT 16571 19301 1.1647456399734475 1.3933250093294156 chrX 155270560 4196394 0.027026333903864327 0.22030611554933685 chrY 59373566 268666 0.004525010338776014 0.17999989557074483