BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236105.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 = 1,449,790 number of mapped reads = 1,153,398 (79.56%) number of supplementary alignments = 7,855 (0.54%) number of secondary alignments = 0 number of mapped bases = 74,363,594 bp number of sequenced bases = 74,325,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,230 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2022 >>>>>>> ACTG content number of A's = 20,990,038 bp (28.24%) number of C's = 13,524,195 bp (18.2%) number of T's = 22,875,783 bp (30.78%) number of G's = 16,934,803 bp (22.78%) number of N's = 650 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 640,317 number of insertions = 6,353 mapped reads with insertion percentage = 0.55% number of deletions = 21,840 mapped reads with deletion percentage = 1.87% homopolymer indels = 45.84% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2594X There is a 2.22% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 6421990 0.025765191573986088 0.3893742597037478 chr2 243199373 5484077 0.022549716853094023 0.30225529391559003 chr3 198022430 6206878 0.031344317913884805 0.18626884476638925 chr4 191154276 3736278 0.01954587717409994 0.16315688670131548 chr5 180915260 3874138 0.021414102934158234 0.15421804262699057 chr6 171115067 7584961 0.044326669375058594 0.31807819057462333 chr7 159138663 4065839 0.025549033298086714 0.3439338670357636 chr8 146364022 5273344 0.03602896345660684 0.44262185351137595 chr9 141213431 3063400 0.021693403936910223 0.24927645706115936 chr10 135534747 2689072 0.019840462018201135 0.23609059776291905 chr11 135006516 2956748 0.021900779959390996 0.21608360272062152 chr12 133851895 2476451 0.018501426520707832 0.14658775764140616 chr13 115169878 2622587 0.02277146633775196 0.1583611033814904 chr14 107349540 2290443 0.02133630940570402 0.16995303156602887 chr15 102531392 1708539 0.01666356972896652 0.1403150339627822 chr16 90354753 1609527 0.017813418182881867 0.17295622534634345 chr17 81195210 1649658 0.020317183735345964 0.1745644815800001 chr18 78077248 1939552 0.024841449329771458 0.41748137149211395 chr19 59128983 1453089 0.02457490263277486 0.2875913891527315 chr20 63025520 1360794 0.021591158629075968 0.15813554789429865 chr21 48129895 1274200 0.026474190313525513 0.19175410272116777 chr22 51304566 706735 0.013775284640357351 0.12220748196745478 chrMT 16571 29178 1.7607869169030232 1.7248764402736 chrX 155270560 3680516 0.023703888232257293 0.17905478645190337 chrY 59373566 205600 0.003462820474687338 0.10897094731340727