BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716962.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 = 573,042 number of mapped reads = 535,118 (93.38%) number of supplementary alignments = 14,232 (2.48%) number of secondary alignments = 0 number of mapped bases = 41,523,988 bp number of sequenced bases = 41,507,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,396 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.442 >>>>>>> ACTG content number of A's = 10,400,555 bp (25.06%) number of C's = 8,485,068 bp (20.44%) number of T's = 12,416,112 bp (29.91%) number of G's = 10,204,446 bp (24.58%) number of N's = 1,606 bp (0%) GC percentage = 45.03% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 274,856 number of insertions = 3,658 mapped reads with insertion percentage = 0.67% number of deletions = 7,724 mapped reads with deletion percentage = 1.42% homopolymer indels = 38.96% >>>>>>> Coverage mean coverageData = 0.0134X 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 2605632 0.010453863623473178 0.17329152340355214 chr2 243199373 3471163 0.014272910974980187 0.1521835169858569 chr3 198022430 2989806 0.015098319922647147 0.12918077662679855 chr4 191154276 2456344 0.01285006044018602 0.13448874573157574 chr5 180915260 2719202 0.015030252284964796 0.129233142327573 chr6 171115067 2471383 0.014442813501630455 0.1294520035752141 chr7 159138663 2318710 0.01457037501942567 0.1615265017414662 chr8 146364022 2220321 0.015169855061785607 0.15033360696292858 chr9 141213431 1103804 0.00781656526708143 0.11390622018827991 chr10 135534747 2137635 0.015771859595532355 0.15886848146129726 chr11 135006516 1675195 0.012408252946842951 0.1382228916844812 chr12 133851895 1995742 0.014910076543929392 0.1292359707658052 chr13 115169878 1302204 0.011306810622826222 0.11186961315751658 chr14 107349540 1306246 0.0121681564727711 0.1209604121856552 chr15 102531392 1267936 0.012366319965694018 0.11730350864738825 chr16 90354753 1380873 0.015282793147583504 0.1340044018456051 chr17 81195210 1203942 0.01482774661214621 0.13350964375219956 chr18 78077248 1164248 0.014911488683617538 0.18010614373890932 chr19 59128983 926647 0.01567162080227221 0.15977410790843904 chr20 63025520 1022926 0.01623034605664499 0.13913431387536473 chr21 48129895 581964 0.01209152856036773 0.12425497103943482 chr22 51304566 597612 0.011648319956551235 0.1153937820501614 chrMT 16571 11614 0.7008629533522419 1.0126048518215203 chrX 155270560 2446056 0.015753507941234965 0.13730715661960124 chrY 59373566 146783 0.0024721944442413985 0.08674238239358718