BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716742.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 = 702,876 number of mapped reads = 586,284 (83.41%) number of supplementary alignments = 751 (0.11%) number of secondary alignments = 0 number of mapped bases = 31,864,663 bp number of sequenced bases = 31,856,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,142 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6714 >>>>>>> ACTG content number of A's = 7,015,469 bp (22.02%) number of C's = 6,118,943 bp (19.21%) number of T's = 10,125,396 bp (31.78%) number of G's = 8,595,739 bp (26.98%) number of N's = 639 bp (0%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 204,386 number of insertions = 1,674 mapped reads with insertion percentage = 0.28% number of deletions = 4,922 mapped reads with deletion percentage = 0.83% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.0103X std coverageData = 0.1205X There is a 0.94% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 3172011 0.012726190961024727 0.1443618172434053 chr2 243199373 2772632 0.011400654392312104 0.1557653244843349 chr3 198022430 2091121 0.01056002090268259 0.111419711525056 chr4 191154276 2063892 0.010796996244018104 0.11647898673833633 chr5 180915260 1931571 0.01067666154861674 0.11170984903653078 chr6 171115067 1370274 0.00800790967168309 0.10272479811480556 chr7 159138663 1873305 0.011771526571138781 0.13517715047234177 chr8 146364022 2009398 0.013728770038855587 0.1306267504467924 chr9 141213431 1417774 0.010039937348452358 0.1129557554327955 chr10 135534747 1655483 0.012214454497044953 0.13653852035350358 chr11 135006516 1346565 0.00997407414024372 0.12047837369531557 chr12 133851895 1525355 0.011395841650205999 0.11631087103465464 chr13 115169878 534622 0.004642029750174781 0.07401632150529049 chr14 107349540 996008 0.009278176692699381 0.10602990674868425 chr15 102531392 635961 0.006202597932153306 0.08502674390006458 chr16 90354753 846466 0.009368250943035615 0.11061709740395383 chr17 81195210 1267659 0.01561248502220759 0.1386197162261811 chr18 78077248 831274 0.010646814805767743 0.13044767540465216 chr19 59128983 831556 0.014063424699863348 0.14556812555601673 chr20 63025520 792996 0.012582141329417037 0.1242087656806547 chr21 48129895 444520 0.009235839803930593 0.10839373126589646 chr22 51304566 341457 0.006655489493859084 0.08954271937557294 chrMT 16571 1140 0.06879488262627481 0.30460963144095604 chrX 155270560 1016213 0.00654478865794005 0.08914645808906903 chrY 59373566 95410 0.0016069440733945473 0.05682393835071035