BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524626.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 = 1,788,639 number of mapped reads = 1,659,692 (92.79%) number of supplementary alignments = 3,586 (0.2%) number of secondary alignments = 0 number of mapped bases = 96,997,017 bp number of sequenced bases = 96,966,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,008 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4376 >>>>>>> ACTG content number of A's = 25,000,855 bp (25.78%) number of C's = 18,656,122 bp (19.24%) number of T's = 30,569,182 bp (31.53%) number of G's = 22,739,338 bp (23.45%) number of N's = 639 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 461,903 number of insertions = 6,788 mapped reads with insertion percentage = 0.41% number of deletions = 18,199 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.2813X There is a 2.74% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% 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 9021724 0.03619539226744795 0.48966452637692925 chr2 243199373 8726607 0.03588252260831281 0.3260975739492817 chr3 198022430 6072618 0.030666313912014916 0.19615491405106944 chr4 191154276 4389901 0.02296522521944526 0.19242165105414152 chr5 180915260 5980544 0.033057156151449024 0.20459762332691922 chr6 171115067 6257582 0.03656943897289886 0.2300723826435877 chr7 159138663 5508473 0.03461429734394589 0.36946400780517885 chr8 146364022 8711489 0.05951933324160769 0.3809808179011268 chr9 141213431 3503521 0.02481011172372124 0.24546607703985635 chr10 135534747 4166340 0.03074001385047039 0.26960189582077426 chr11 135006516 6156739 0.045603272956099394 0.2957277649580576 chr12 133851895 3251714 0.024293372910409672 0.18176026127932354 chr13 115169878 2423418 0.021042116585380077 0.16363510749972088 chr14 107349540 1822092 0.016973449536905327 0.15204930119261204 chr15 102531392 2489841 0.024283694500119534 0.18087302367068403 chr16 90354753 2841816 0.03145175993121247 0.2102036285215121 chr17 81195210 2116292 0.02606424689338201 0.18708001217642908 chr18 78077248 2635923 0.03376044965109426 0.40425522726753577 chr19 59128983 1884458 0.031870292780107515 0.3621024709728588 chr20 63025520 1788552 0.028378218854838485 0.19250834624141583 chr21 48129895 856565 0.01779694304340369 0.16260454363831078 chr22 51304566 1674366 0.03263580867246787 0.20202765034867892 chrMT 16571 16679 1.0065174099330154 1.2255033392848131 chrX 155270560 4465559 0.028759856343662314 0.217488471853606 chrY 59373566 234204 0.003944583688977011 0.11446168121268112