BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716632.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 = 2,682,439 number of mapped reads = 1,845,015 (68.78%) number of supplementary alignments = 10,669 (0.4%) number of secondary alignments = 0 number of mapped bases = 105,527,989 bp number of sequenced bases = 105,500,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,492 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0625 >>>>>>> ACTG content number of A's = 26,371,767 bp (25%) number of C's = 18,618,301 bp (17.65%) number of T's = 33,307,758 bp (31.57%) number of G's = 27,200,987 bp (25.78%) number of N's = 1,608 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 527,053 number of insertions = 7,079 mapped reads with insertion percentage = 0.38% number of deletions = 17,797 mapped reads with deletion percentage = 0.96% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.0341X std coverageData = 0.3093X There is a 2.86% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12809801 0.05139325610747425 0.5785383176409258 chr2 243199373 9590699 0.03943554163686105 0.4445545821639939 chr3 198022430 6934044 0.035016457479084565 0.22189016712650203 chr4 191154276 4315768 0.022577407580461343 0.19188700643679218 chr5 180915260 4428368 0.024477581382576573 0.18372524297455906 chr6 171115067 7286150 0.042580411694547037 0.2657466991845653 chr7 159138663 7294642 0.045838276271053 0.3891513218179776 chr8 146364022 5794033 0.03958645656785791 0.26327910854226605 chr9 141213431 4334519 0.03069480692668674 0.25318913226079953 chr10 135534747 5603271 0.041341951964539395 0.3149614362575116 chr11 135006516 3621525 0.02682481636664115 0.25507785903227614 chr12 133851895 4190555 0.03130740136327543 0.2091454671808035 chr13 115169878 2096965 0.018207582020708574 0.15629766802219847 chr14 107349540 2301342 0.02143783755384513 0.18115061663395474 chr15 102531392 2357771 0.022995601191096674 0.18159042071039877 chr16 90354753 2332407 0.025813882751690994 0.20320104637093858 chr17 81195210 2853325 0.03514154344819109 0.2296006832004148 chr18 78077248 3417672 0.04377295675175436 0.3979535558097491 chr19 59128983 3092581 0.05230228634238475 0.4114696578586911 chr20 63025520 1725848 0.027383320280419742 0.19542166456398213 chr21 48129895 1307298 0.027161871015924717 0.2023649622341455 chr22 51304566 1513743 0.02950503469808126 0.20270538983213288 chrMT 16571 62200 3.753545350310784 2.7802793681241122 chrX 155270560 6013095 0.038726562202132844 0.25838800262208106 chrY 59373566 250367 0.004216809211021619 0.10448091717609627