BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174002.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,096,982 number of mapped reads = 2,050,199 (97.77%) number of supplementary alignments = 186,649 (8.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,025,864 number of mapped paired reads (second in pair) = 1,024,335 number of mapped paired reads (both in pair) = 2,018,916 number of mapped paired reads (singletons) = 31,283 number of mapped bases = 242,907,037 bp number of sequenced bases = 242,769,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,523,422 duplication rate = 63.11% >>>>>>> Insert size mean insert size = 1,041,484.5431 std insert size = 9,539,580.7244 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.287 >>>>>>> ACTG content number of A's = 73,277,298 bp (30.18%) number of C's = 47,361,501 bp (19.51%) number of T's = 73,089,293 bp (30.11%) number of G's = 49,038,385 bp (20.2%) number of N's = 2,536 bp (0%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,371,248 number of insertions = 26,066 mapped reads with insertion percentage = 1.23% number of deletions = 58,998 mapped reads with deletion percentage = 2.81% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.0785X std coverageData = 1.2642X There is a 1.85% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 19321402 0.07751796935342439 0.8840861560919239 chr2 243199373 22491312 0.09248096211169098 3.439545072588743 chr3 198022430 16461520 0.0831295727458753 0.7997071717371906 chr4 191154276 16672077 0.08721791292808956 0.9099021617611563 chr5 180915260 15412032 0.08518923168780787 0.8060401362279394 chr6 171115067 14549226 0.0850259784546033 0.8490390473238786 chr7 159138663 13389970 0.0841402695459368 0.968578210185577 chr8 146364022 12542254 0.08569219285324094 1.0609392437452798 chr9 141213431 10192376 0.07217710049124151 0.8494666286654444 chr10 135534747 11901033 0.08780798476718299 1.06049458334485 chr11 135006516 10655311 0.07892442021094745 0.7913990329723665 chr12 133851895 11159295 0.08337046703746705 0.8055030381469045 chr13 115169878 8357301 0.0725649896060496 0.7565793305811211 chr14 107349540 7575511 0.07056863960479011 0.7381757143425514 chr15 102531392 7170718 0.06993680530544245 0.7243800188845435 chr16 90354753 6912216 0.07650085657364367 0.8039599519199933 chr17 81195210 6650669 0.0819096225011303 0.8421350965848519 chr18 78077248 6777057 0.0867993836053238 1.1310456942625824 chr19 59128983 4240329 0.07171320704095316 0.783242443649076 chr20 63025520 5382996 0.08540978321162603 0.8225893810151352 chr21 48129895 3478092 0.07226469120699308 0.9110094093995801 chr22 51304566 2940536 0.057315288467697005 0.6878016768374449 chrMT 16571 176649 10.660129141270895 11.082734469012228 chrX 155270560 6703665 0.04317408915122094 0.5655771775257699 chrY 59373566 1793490 0.03020687691219355 0.5611367093106796