BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716207.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 = 4,726,156 number of mapped reads = 4,295,674 (90.89%) number of supplementary alignments = 101,084 (2.14%) number of secondary alignments = 0 number of mapped bases = 321,923,965 bp number of sequenced bases = 321,807,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 240,333 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1277 >>>>>>> ACTG content number of A's = 85,061,358 bp (26.43%) number of C's = 65,020,736 bp (20.2%) number of T's = 97,854,252 bp (30.41%) number of G's = 73,831,712 bp (22.94%) number of N's = 39,391 bp (0.01%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,416,207 number of insertions = 27,495 mapped reads with insertion percentage = 0.63% number of deletions = 68,045 mapped reads with deletion percentage = 1.56% homopolymer indels = 39.72% >>>>>>> Coverage mean coverageData = 0.104X std coverageData = 0.7755X There is a 7.83% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 25369513 0.10178314861650836 0.9024626438439733 chr2 243199373 27808698 0.11434527012534691 1.23984621901725 chr3 198022430 21555775 0.10885521907796 0.4189756688439487 chr4 191154276 21004552 0.10988272111684282 0.4922946919235736 chr5 180915260 19688850 0.10882912806802478 0.4297797920385153 chr6 171115067 18742535 0.10953176320820422 0.5365717130925354 chr7 159138663 17574055 0.11043234037978565 1.0285609937084674 chr8 146364022 16684182 0.11399100524854394 1.0756738228778313 chr9 141213431 13489402 0.09552492213010531 0.859497425654256 chr10 135534747 15018620 0.11081010834808287 0.7294948943694842 chr11 135006516 14545343 0.10773808132342294 0.8738175263073649 chr12 133851895 14624479 0.10925866234467581 0.43879494537473285 chr13 115169878 10351884 0.08988360654510721 0.37919043277440573 chr14 107349540 9568670 0.08913564045081143 0.5531306864048238 chr15 102531392 9177237 0.08950660691312959 0.3866158232292699 chr16 90354753 9287304 0.1027871107123717 0.4959441426553757 chr17 81195210 8609441 0.106033853474854 0.49705970462322013 chr18 78077248 8958562 0.11473972545753662 1.7219772299375602 chr19 59128983 6264173 0.1059408209337881 0.7753002817055912 chr20 63025520 6679581 0.10598216405037197 0.4604360259070887 chr21 48129895 4186969 0.08699310480523591 0.44346118719640815 chr22 51304566 3512677 0.06846714189142541 0.3318482903397752 chrMT 16571 16429 0.99143081286585 1.5901449400181544 chrX 155270560 18405314 0.11853704913539309 0.6568340237569437 chrY 59373566 799720 0.013469293725763415 0.3642650953925771