BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504736.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,174,621 number of mapped reads = 1,923,243 (88.44%) number of secondary alignments = 0 number of mapped bases = 61,536,586 bp number of sequenced bases = 61,536,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 417,533 duplication rate = 8.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.3009 >>>>>>> ACTG content number of A's = 17,874,451 bp (29.05%) number of C's = 12,172,825 bp (19.78%) number of T's = 19,044,585 bp (30.95%) number of G's = 12,444,631 bp (20.22%) number of N's = 94 bp (0%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 33,465 >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 1.4035X There is a 0.95% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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% 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 4783730 0.019192449674979947 0.5625111201634928 chr2 243199373 4244284 0.01745187065099876 0.27449111517783614 chr3 198022430 3961574 0.020005683194575484 0.38131668901337035 chr4 191154276 3476964 0.018189307991206015 0.32582358262056726 chr5 180915260 3941622 0.021787117349857606 0.4160753059110325 chr6 171115067 3444058 0.020127146372212797 0.3709038683969221 chr7 159138663 3290032 0.020673995482794773 0.4406280540782064 chr8 146364022 9093210 0.06212735804704793 5.683018715323967 chr9 141213431 2623412 0.01857763798685693 0.42240865315489723 chr10 135534747 2215284 0.01634476803206782 0.3046857677651021 chr11 135006516 2532966 0.018761805541296986 0.29987010832692 chr12 133851895 2828254 0.0211297270016237 0.5982577588865303 chr13 115169878 4944540 0.042932579992834584 2.8977643228014096 chr14 107349540 1782802 0.01660744890010707 0.33059910167216167 chr15 102531392 1553022 0.015146795237111382 0.3729395500839873 chr16 90354753 915032 0.010127104215535844 0.18220878018652026 chr17 81195210 773642 0.00952817290576624 0.204006421903637 chr18 78077248 1164538 0.014915202953874603 0.2658831370780117 chr19 59128983 427684 0.007233068764264049 0.1420271354419318 chr20 63025520 1005760 0.015957980195958718 0.34653879113917047 chr21 48129895 440522 0.009152772928343185 0.19358708539846706 chr22 51304566 326820 0.006370193249466334 0.1497578090221369 chrMT 16571 0 0.0 0.0 chrX 155270560 1064380 0.006855002004243432 0.3518570588418254 chrY 59373566 702454 0.011831089950029277 0.28825621226029874