BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524942.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 = 1,435,421 number of mapped reads = 1,331,470 (92.76%) number of supplementary alignments = 3,350 (0.23%) number of secondary alignments = 0 number of mapped bases = 77,775,880 bp number of sequenced bases = 77,750,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,016 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7097 >>>>>>> ACTG content number of A's = 19,518,436 bp (25.1%) number of C's = 14,312,034 bp (18.41%) number of T's = 24,866,947 bp (31.98%) number of G's = 19,052,486 bp (24.5%) number of N's = 911 bp (0%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 376,397 number of insertions = 5,965 mapped reads with insertion percentage = 0.45% number of deletions = 14,656 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2425X There is a 2.29% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8598095 0.034495781657450715 0.45115930680154975 chr2 243199373 7010218 0.028824983853885183 0.27542263031842007 chr3 198022430 4572504 0.02309083874993353 0.1633012972313803 chr4 191154276 5396934 0.028233394057059963 0.19141934946247474 chr5 180915260 3317939 0.01833974093727638 0.1482523062602809 chr6 171115067 3802108 0.022219597997176953 0.23286044594304825 chr7 159138663 5274304 0.03314281960506354 0.33391957988140014 chr8 146364022 5009350 0.03422528249462836 0.24819371057704676 chr9 141213431 2343739 0.01659713940382909 0.1914188374651064 chr10 135534747 4101475 0.030261428089728162 0.2475156051298186 chr11 135006516 3454666 0.02558888342841171 0.22060579777540534 chr12 133851895 4488339 0.03353212892503315 0.19722004496900897 chr13 115169878 1626121 0.014119325541006478 0.12899126408025496 chr14 107349540 1882522 0.017536376960721023 0.1453891855985125 chr15 102531392 2302793 0.02245939467982645 0.16935419065893384 chr16 90354753 2032214 0.02249150080682529 0.1689434409125883 chr17 81195210 2016687 0.024837511966531032 0.21082371957174453 chr18 78077248 1644974 0.021068544833957262 0.30457234819365403 chr19 59128983 1723676 0.029151118665443645 0.2802309106618741 chr20 63025520 1404249 0.022280641238660148 0.16156110258021864 chr21 48129895 1169023 0.02428891648319615 0.17179761000053267 chr22 51304566 875397 0.017062750321287193 0.13919477268986963 chrMT 16571 8305 0.5011767545712389 0.7926984002410649 chrX 155270560 3513571 0.022628700508325595 0.18594134284076427 chrY 59373566 206677 0.0034809598601505593 0.09606861857335282