BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716973.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 = 789,583 number of mapped reads = 696,409 (88.2%) number of supplementary alignments = 3,484 (0.44%) number of secondary alignments = 0 number of mapped bases = 40,094,505 bp number of sequenced bases = 40,082,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,603 duplication rate = 1.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6588 >>>>>>> ACTG content number of A's = 10,074,457 bp (25.13%) number of C's = 7,296,703 bp (18.2%) number of T's = 12,437,905 bp (31.03%) number of G's = 10,272,618 bp (25.63%) number of N's = 613 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 202,351 number of insertions = 2,803 mapped reads with insertion percentage = 0.4% number of deletions = 7,673 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 0.1468X There is a 1.22% of reference with a coverageData >= 1X There is a 0.05% 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 3435691 0.013784082006359374 0.17042398753283242 chr2 243199373 4170382 0.01714799651231009 0.18815133898232497 chr3 198022430 3005574 0.01517794726587286 0.13112693351286728 chr4 191154276 2396663 0.012537846655337179 0.11869896988163166 chr5 180915260 2250179 0.012437751243316898 0.1161216713041332 chr6 171115067 2286592 0.013362891065577528 0.1261281701100181 chr7 159138663 2108688 0.013250632877316558 0.26987875158257296 chr8 146364022 2948300 0.020143611522235975 0.1634580253838901 chr9 141213431 1382927 0.009793169036449514 0.11363031118171923 chr10 135534747 1982010 0.014623630057021466 0.1778887973058832 chr11 135006516 1420444 0.010521299579347712 0.12002829991383065 chr12 133851895 1770384 0.01322643956590977 0.12204437883082005 chr13 115169878 1135578 0.009860026073831562 0.10343409983628249 chr14 107349540 1023771 0.009536799133000477 0.10380268748117454 chr15 102531392 999639 0.00974958966713336 0.10306304580766583 chr16 90354753 1145189 0.012674363682893361 0.12179377895410648 chr17 81195210 1305848 0.01608282064914913 0.1331624336670231 chr18 78077248 1035800 0.013266348731963504 0.16408604892592887 chr19 59128983 815785 0.013796702710073671 0.1658664783103664 chr20 63025520 928402 0.014730572631530846 0.127914148681942 chr21 48129895 436597 0.009071222781599669 0.10013802081001623 chr22 51304566 543203 0.010587810059634849 0.10706081525414748 chrMT 16571 3734 0.22533341379518435 0.5280500216370043 chrX 155270560 1477393 0.009514958920738097 0.10863095825037715 chrY 59373566 85732 0.0014439422419061034 0.04507084660498194