BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717062.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 = 966,604 number of mapped reads = 756,965 (78.31%) number of supplementary alignments = 2,641 (0.27%) number of secondary alignments = 0 number of mapped bases = 41,781,475 bp number of sequenced bases = 41,769,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,885 duplication rate = 1.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.3187 >>>>>>> ACTG content number of A's = 9,776,743 bp (23.41%) number of C's = 8,180,935 bp (19.59%) number of T's = 13,008,425 bp (31.14%) number of G's = 10,802,661 bp (25.86%) number of N's = 1,215 bp (0%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 222,917 number of insertions = 3,017 mapped reads with insertion percentage = 0.4% number of deletions = 6,860 mapped reads with deletion percentage = 0.9% homopolymer indels = 35.17% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 0.1403X There is a 1.25% 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 4032733 0.01617943010059742 0.16869469256351505 chr2 243199373 3567914 0.014670736836151301 0.17239732422543785 chr3 198022430 2803380 0.014156881116952257 0.13042119546596223 chr4 191154276 2662226 0.013927106710393442 0.13931547790536314 chr5 180915260 2529569 0.013982065415598441 0.12648316997962744 chr6 171115067 1781019 0.010408311969395425 0.11036962839282902 chr7 159138663 2358247 0.014818818730430078 0.15424306204368468 chr8 146364022 2592780 0.017714599288614793 0.14931209485744917 chr9 141213431 1805128 0.012782976712746254 0.12765470224900352 chr10 135534747 2158023 0.015922285965531777 0.1874583559497196 chr11 135006516 1693825 0.01254624628636443 0.13918179340465142 chr12 133851895 1982104 0.014808187810863642 0.13006536237968036 chr13 115169878 722130 0.006270129069686086 0.08392073119336126 chr14 107349540 1857202 0.017300511953754063 0.1428526845245106 chr15 102531392 808413 0.007884541351003993 0.09567585646564741 chr16 90354753 1105493 0.012235028742760218 0.12382496564741427 chr17 81195210 1596666 0.019664534398026682 0.15450130917517632 chr18 78077248 1080924 0.013844289183963042 0.1544646664108436 chr19 59128983 1082664 0.018310208379535294 0.16958070578513018 chr20 63025520 1054782 0.016735792104531626 0.14385906478205335 chr21 48129895 554817 0.01152749242440691 0.12061660253467613 chr22 51304566 466908 0.009100710451385555 0.10596638919977322 chrMT 16571 2925 0.1765131856858367 0.4424995610816756 chrX 155270560 1348716 0.008686231311331652 0.10587447081175701 chrY 59373566 132887 0.002238150896983348 0.07746080706590998