BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717029.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 = 439,474 number of mapped reads = 393,457 (89.53%) number of supplementary alignments = 1,791 (0.41%) number of secondary alignments = 0 number of mapped bases = 22,956,107 bp number of sequenced bases = 22,949,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,895 duplication rate = 1.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5932 >>>>>>> ACTG content number of A's = 5,959,804 bp (25.97%) number of C's = 4,404,018 bp (19.19%) number of T's = 7,245,134 bp (31.57%) number of G's = 5,340,040 bp (23.27%) number of N's = 308 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 114,027 number of insertions = 1,753 mapped reads with insertion percentage = 0.44% number of deletions = 4,392 mapped reads with deletion percentage = 1.11% homopolymer indels = 39.8% >>>>>>> Coverage mean coverageData = 0.0074X std coverageData = 0.1057X There is a 0.71% of reference with a coverageData >= 1X There is a 0.02% 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 1910343 0.007664345999763828 0.1301681377054303 chr2 243199373 2299676 0.00945592898383007 0.11822066291548859 chr3 198022430 1746120 0.008817788974713622 0.0975670007644871 chr4 191154276 1309387 0.006849896467918929 0.0873759086831644 chr5 180915260 1145862 0.0063336945705962005 0.08130357300600664 chr6 171115067 1279164 0.007475460942314331 0.09008213979629336 chr7 159138663 1440879 0.009054235927569657 0.19479259620882755 chr8 146364022 1731071 0.0118271620057011 0.12560990332930025 chr9 141213431 962365 0.006814967904858852 0.08925050334360587 chr10 135534747 1080681 0.007973460857236853 0.12000488644953343 chr11 135006516 686370 0.005083976835606957 0.07824394235318627 chr12 133851895 1077077 0.008046781855423115 0.09538444642787276 chr13 115169878 604173 0.005245928974588304 0.0739982429721189 chr14 107349540 582387 0.005425146675057946 0.07544296960495542 chr15 102531392 542791 0.005293900623137936 0.07480396464665387 chr16 90354753 683743 0.007567316353573564 0.09108757300218272 chr17 81195210 935226 0.011518241039095779 0.11102932752016519 chr18 78077248 529476 0.006781437788381066 0.10560836884425366 chr19 59128983 462194 0.007816708093897031 0.12314330488492478 chr20 63025520 506391 0.008034697690713221 0.09313849342674835 chr21 48129895 229822 0.004775036388506561 0.07198310958696263 chr22 51304566 337083 0.006570233924208618 0.08295576600567253 chrMT 16571 25925 1.5644801158650654 1.4649079798371005 chrX 155270560 795457 0.0051230381342090864 0.07709173335231341 chrY 59373566 52444 8.832887012378539E-4 0.035454472377576395