BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716271.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 = 718,725 number of mapped reads = 638,882 (88.89%) number of supplementary alignments = 2,950 (0.41%) number of secondary alignments = 0 number of mapped bases = 36,296,136 bp number of sequenced bases = 36,286,416 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,506 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1149 >>>>>>> ACTG content number of A's = 9,140,304 bp (25.19%) number of C's = 7,276,622 bp (20.05%) number of T's = 11,131,051 bp (30.68%) number of G's = 8,737,626 bp (24.08%) number of N's = 813 bp (0%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 181,511 number of insertions = 2,553 mapped reads with insertion percentage = 0.4% number of deletions = 5,643 mapped reads with deletion percentage = 0.88% homopolymer indels = 39.65% >>>>>>> Coverage mean coverageData = 0.0117X std coverageData = 0.1287X There is a 1.11% of reference with a coverageData >= 1X There is a 0.04% 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 2919812 0.011714361987487284 0.17494367622644752 chr2 243199373 3097297 0.01273562905114891 0.14160486235818862 chr3 198022430 2407585 0.012158142893206592 0.11410268611980948 chr4 191154276 2327057 0.01217371145806856 0.12067314524411644 chr5 180915260 2159461 0.011936312061237951 0.11370483972917422 chr6 171115067 2061186 0.012045613727282122 0.11632761729326184 chr7 159138663 2001954 0.012579934770471209 0.13944304934801477 chr8 146364022 1831492 0.012513266409145275 0.1253962071978323 chr9 141213431 1524889 0.010798470012388553 0.12926935662795827 chr10 135534747 1723046 0.012712946592212254 0.13149220127714284 chr11 135006516 1644830 0.012183337876817739 0.131831093027319 chr12 133851895 1726540 0.012898883501051665 0.11908622086371543 chr13 115169878 1117168 0.009700175248948341 0.10151978540575098 chr14 107349540 1092092 0.010173234091175426 0.10828167165585428 chr15 102531392 1039456 0.010137929269506065 0.1039651273796366 chr16 90354753 1065250 0.01178963988756629 0.11707235659570674 chr17 81195210 1001190 0.012330653495446344 0.11833943903671071 chr18 78077248 963434 0.012339497416712229 0.18842988689517498 chr19 59128983 738635 0.012491928027918221 0.1370111862418043 chr20 63025520 799014 0.012677626459884822 0.11895550962823465 chr21 48129895 464818 0.009657573530962409 0.10757633273889661 chr22 51304566 430609 0.008393190578787861 0.0951787320199927 chrMT 16571 738 0.04453563454227265 0.20628187462351066 chrX 155270560 2048205 0.013191199928692212 0.1270506692907279 chrY 59373566 110378 0.0018590427935556372 0.05438502264554732