BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716376.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 = 1,862,380 number of mapped reads = 1,736,453 (93.24%) number of supplementary alignments = 35,371 (1.9%) number of secondary alignments = 0 number of mapped bases = 137,369,184 bp number of sequenced bases = 137,304,283 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,957 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4536 >>>>>>> ACTG content number of A's = 35,187,610 bp (25.63%) number of C's = 26,537,631 bp (19.33%) number of T's = 42,608,827 bp (31.03%) number of G's = 32,960,286 bp (24.01%) number of N's = 9,929 bp (0.01%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 915,884 number of insertions = 10,948 mapped reads with insertion percentage = 0.62% number of deletions = 33,531 mapped reads with deletion percentage = 1.9% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 0.4242X There is a 3.82% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13667503 0.0548343789281873 0.9355365880413251 chr2 243199373 11389198 0.04683070461698929 0.42980786489784384 chr3 198022430 9251970 0.04672182843125398 0.2398016744771568 chr4 191154276 8820640 0.046144089395102 0.30386204196315386 chr5 180915260 7726742 0.04270917776643054 0.23169210119706554 chr6 171115067 7734813 0.04520240757057355 0.25573647867977 chr7 159138663 7354113 0.046211981811107715 0.46890874365190666 chr8 146364022 6823909 0.04662285790424644 0.49529864091332676 chr9 141213431 5529129 0.03915441301047349 0.33277819223967264 chr10 135534747 6223176 0.04591572373688055 0.38441871795295435 chr11 135006516 6394348 0.047363254674315125 0.3841136664604818 chr12 133851895 6397717 0.04779698486898523 0.24484939540056225 chr13 115169878 4740874 0.04116418357237472 0.22757126210066525 chr14 107349540 3793816 0.03534077556364005 0.22698497175775703 chr15 102531392 3799217 0.03705418336659274 0.2140894158865759 chr16 90354753 3098291 0.03429029350564436 0.23228559359127735 chr17 81195210 3996759 0.049224073686120154 0.28750679268244367 chr18 78077248 3646179 0.046699635212552576 0.6210630529322133 chr19 59128983 2675874 0.04525486257729141 0.6105248262213232 chr20 63025520 2812735 0.044628509213410696 0.25347092237392305 chr21 48129895 1853789 0.038516373243698124 0.2616572883949469 chr22 51304566 1580699 0.03081010372449111 0.1959587514503971 chrMT 16571 230906 13.934343129563695 8.178087537140573 chrX 155270560 7408760 0.04771516248798227 0.2845128670303543 chrY 59373566 418027 0.007040624779047295 0.2383420009275785