BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716442.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 = 703,797 number of mapped reads = 596,971 (84.82%) number of supplementary alignments = 3,098 (0.44%) number of secondary alignments = 0 number of mapped bases = 34,337,313 bp number of sequenced bases = 34,328,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,494 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5632 >>>>>>> ACTG content number of A's = 8,868,654 bp (25.83%) number of C's = 6,574,312 bp (19.15%) number of T's = 10,825,775 bp (31.54%) number of G's = 8,059,490 bp (23.48%) number of N's = 268 bp (0%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 171,638 number of insertions = 2,309 mapped reads with insertion percentage = 0.39% number of deletions = 5,597 mapped reads with deletion percentage = 0.93% homopolymer indels = 41.15% >>>>>>> Coverage mean coverageData = 0.0111X std coverageData = 0.1314X There is a 1.05% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 3838175 0.015398858324208549 0.17309544882190359 chr2 243199373 3414909 0.014041602812849358 0.17879220809827584 chr3 198022430 2223111 0.0112265615566883 0.11031504632544975 chr4 191154276 1514253 0.007921627659535066 0.09888256217446699 chr5 180915260 2504294 0.013842359124376794 0.12287800714747983 chr6 171115067 1300624 0.007600873627335225 0.09531291446633446 chr7 159138663 2397132 0.015063165385522938 0.1894259948234087 chr8 146364022 1584351 0.010824729864283178 0.12203445228620537 chr9 141213431 957332 0.006779326819132381 0.1011948650624547 chr10 135534747 1582874 0.011678732096648249 0.12384080350621235 chr11 135006516 1450186 0.010741600057289087 0.13266832773656698 chr12 133851895 1336491 0.009984849299294567 0.10441006094486999 chr13 115169878 1005809 0.008733264439161774 0.09712544311808355 chr14 107349540 745304 0.006942777770635999 0.08897374690387315 chr15 102531392 1521592 0.014840254972837977 0.12747331369374484 chr16 90354753 956870 0.01059014571153772 0.11043329949824009 chr17 81195210 1279346 0.01575642208450474 0.13457480211795328 chr18 78077248 1089833 0.013958394127825817 0.21488361279438953 chr19 59128983 536786 0.009078221419773108 0.12466240947769859 chr20 63025520 874903 0.013881726005592655 0.12309586036558405 chr21 48129895 395334 0.0082138969968665 0.09649160716139707 chr22 51304566 450161 0.008774287263242808 0.09793730461938466 chrMT 16571 3369 0.2033069820771227 0.491313647355103 chrX 155270560 1298102 0.008360258377376884 0.10311932502441255 chrY 59373566 76172 0.0012829278268379567 0.044815838844405875