BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716940.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 = 579,862 number of mapped reads = 450,945 (77.77%) number of supplementary alignments = 623 (0.11%) number of secondary alignments = 0 number of mapped bases = 24,340,998 bp number of sequenced bases = 24,334,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,122 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7948 >>>>>>> ACTG content number of A's = 5,337,727 bp (21.94%) number of C's = 4,684,463 bp (19.25%) number of T's = 7,671,944 bp (31.53%) number of G's = 6,639,645 bp (27.29%) number of N's = 453 bp (0%) GC percentage = 46.54% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 158,772 number of insertions = 1,315 mapped reads with insertion percentage = 0.29% number of deletions = 3,844 mapped reads with deletion percentage = 0.85% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1036X There is a 0.71% of reference with a coverageData >= 1X There is a 0.06% 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 2390315 0.009590006197015654 0.11838705231027495 chr2 243199373 2121694 0.008724093215487031 0.12677333158380738 chr3 198022430 1668786 0.00842725745765265 0.10058528886238909 chr4 191154276 1579433 0.008262608784121574 0.10239322156048808 chr5 180915260 1457361 0.008055489625363831 0.09802618501475525 chr6 171115067 1016393 0.005939821769172436 0.08886889322400321 chr7 159138663 1393553 0.008756847479609654 0.10944616104337566 chr8 146364022 1534132 0.010481619588179942 0.11704662529738155 chr9 141213431 1061360 0.0075159989562182655 0.09717424266420052 chr10 135534747 1235343 0.0091145852066998 0.11700674764972356 chr11 135006516 1051762 0.007790453610402035 0.10248690349640953 chr12 133851895 1202939 0.008987089798018922 0.10505586255643204 chr13 115169878 430616 0.0037389637592565653 0.06667477998997118 chr14 107349540 777557 0.007243226193610145 0.09336962528701642 chr15 102531392 470494 0.004588779990424786 0.07372853122305165 chr16 90354753 662011 0.0073267977391294516 0.09920220279051337 chr17 81195210 963813 0.011870318458441083 0.12294238315034035 chr18 78077248 640368 0.00820172350336938 0.10671151596590188 chr19 59128983 635647 0.01075017644054524 0.13591255158939394 chr20 63025520 633203 0.010046771530008797 0.11382726814991613 chr21 48129895 341593 0.007097314465365029 0.09577441007575424 chr22 51304566 263570 0.005137359509093206 0.08156063052525661 chrMT 16571 849 0.05123408364009414 0.262919996053931 chrX 155270560 733783 0.004725834697833253 0.07583407695376802 chrY 59373566 74423 0.0012534702732862634 0.04983295959234699