BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716893.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,936,333 number of mapped reads = 3,674,213 (93.34%) number of supplementary alignments = 81,046 (2.06%) number of secondary alignments = 0 number of mapped bases = 270,109,820 bp number of sequenced bases = 270,020,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,448 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9597 >>>>>>> ACTG content number of A's = 70,165,878 bp (25.99%) number of C's = 56,857,426 bp (21.06%) number of T's = 77,076,231 bp (28.54%) number of G's = 65,890,666 bp (24.4%) number of N's = 30,436 bp (0.01%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,973,445 number of insertions = 19,624 mapped reads with insertion percentage = 0.53% number of deletions = 52,261 mapped reads with deletion percentage = 1.41% homopolymer indels = 41.56% >>>>>>> Coverage mean coverageData = 0.0873X std coverageData = 0.6095X There is a 6.86% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21661423 0.08690619470913977 0.7061418023731755 chr2 243199373 22995715 0.09455499295222278 0.9047242987052275 chr3 198022430 17881528 0.09030051797667567 0.36482116136856213 chr4 191154276 17017758 0.0890263004108786 0.4077501566159538 chr5 180915260 16189636 0.08948739868599255 0.3711387461943998 chr6 171115067 15460951 0.09035411826125166 0.4485628416338354 chr7 159138663 14818536 0.09311713269829344 0.7896588624299439 chr8 146364022 13855062 0.09466166487280597 0.8391729711495505 chr9 141213431 11339732 0.08030207834834067 0.6630170906197003 chr10 135534747 12876947 0.09500845565454887 0.5862984291198954 chr11 135006516 12156829 0.09004623895338504 0.6715224295309857 chr12 133851895 12466228 0.09313449017662395 0.38484635547411145 chr13 115169878 8550231 0.07424016720760962 0.33090404355339836 chr14 107349540 8216328 0.07653808297641518 0.4485039883196066 chr15 102531392 7789617 0.07597299566556162 0.33882971488986924 chr16 90354753 8091179 0.08954901354220957 0.4338897547128545 chr17 81195210 7481039 0.09213645731072066 0.4207378731385307 chr18 78077248 7423373 0.09507728807244846 1.354771377987727 chr19 59128983 5577283 0.09432401365672059 0.662768906388478 chr20 63025520 5795992 0.09196262085580571 0.3966168111107767 chr21 48129895 3554703 0.07385644618588925 0.3795680097469767 chr22 51304566 3189250 0.06216308310648218 0.3068114862546719 chrMT 16571 13452 0.8117796149900428 1.2213759186187254 chrX 155270560 15032236 0.09681317565931365 0.5320097283277332 chrY 59373566 674792 0.01136519238207791 0.28358635429260803