BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716622.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 = 2,004,250 number of mapped reads = 1,835,597 (91.59%) number of supplementary alignments = 8,042 (0.4%) number of secondary alignments = 0 number of mapped bases = 105,409,454 bp number of sequenced bases = 105,383,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,497 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7141 >>>>>>> ACTG content number of A's = 26,534,323 bp (25.18%) number of C's = 21,286,451 bp (20.2%) number of T's = 32,199,366 bp (30.55%) number of G's = 25,360,877 bp (24.07%) number of N's = 2,276 bp (0%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 505,162 number of insertions = 7,616 mapped reads with insertion percentage = 0.41% number of deletions = 15,333 mapped reads with deletion percentage = 0.83% homopolymer indels = 39.75% >>>>>>> Coverage mean coverageData = 0.0341X std coverageData = 0.2654X There is a 2.98% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10351295 0.041529665837823526 0.3954803825314254 chr2 243199373 8190372 0.033677603272439356 0.30687057100286536 chr3 198022430 6487212 0.03275998582584811 0.2023760881037775 chr4 191154276 6071632 0.031762993363538466 0.2209541247467753 chr5 180915260 4068889 0.022490579291100155 0.17015377675334512 chr6 171115067 7038980 0.04113594508892662 0.23972504141198644 chr7 159138663 6639461 0.04172123150236596 0.3026567140003455 chr8 146364022 5606537 0.03830543137165225 0.250001433367675 chr9 141213431 4987041 0.03531562801558161 0.2857093607856037 chr10 135534747 5811132 0.04287558820617417 0.2904266482931153 chr11 135006516 5425243 0.04018504558698485 0.2892259778920829 chr12 133851895 5608477 0.04190061709623162 0.23078696968416929 chr13 115169878 2372637 0.020601194003175033 0.15855175328113308 chr14 107349540 3158502 0.029422594638039437 0.20529044250576436 chr15 102531392 3022402 0.02947782080243288 0.19138507379908432 chr16 90354753 2691892 0.02979247810018362 0.2094548971917658 chr17 81195210 3010551 0.037077938464596616 0.2265566390097063 chr18 78077248 3414110 0.043727335266734814 0.49716746497743886 chr19 59128983 2528152 0.04275656153260745 0.30206555428867177 chr20 63025520 2508774 0.039805685062177985 0.23075226689249595 chr21 48129895 1353439 0.0281205475308018 0.21287059886439355 chr22 51304566 1528733 0.029797211421689056 0.19302926562644918 chrMT 16571 7039 0.4247782270231127 0.8029889405816364 chrX 155270560 3241265 0.020874948863454864 0.19723043461017503 chrY 59373566 285687 0.004811686736147867 0.11967335086196014