BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524938.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 = 768,316 number of mapped reads = 711,468 (92.6%) number of supplementary alignments = 2,883 (0.38%) number of secondary alignments = 0 number of mapped bases = 41,286,631 bp number of sequenced bases = 41,273,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,739 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7953 >>>>>>> ACTG content number of A's = 10,188,436 bp (24.69%) number of C's = 7,706,247 bp (18.67%) number of T's = 13,330,083 bp (32.3%) number of G's = 10,047,906 bp (24.34%) number of N's = 378 bp (0%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 204,318 number of insertions = 3,061 mapped reads with insertion percentage = 0.43% number of deletions = 8,020 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 0.1556X There is a 1.23% 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 4568069 0.018327212111539735 0.2720288078480282 chr2 243199373 3518192 0.014466287295896935 0.17642906115737692 chr3 198022430 2614521 0.013203155824317478 0.12171118345295985 chr4 191154276 1872193 0.009794146587649443 0.12092941710530826 chr5 180915260 2552568 0.014109191231298012 0.12621910010949836 chr6 171115067 2677584 0.015647856421667414 0.13732502110820777 chr7 159138663 2550552 0.016027230290353765 0.182744239549666 chr8 146364022 3611145 0.024672354248368496 0.19753628792062491 chr9 141213431 1485376 0.010518659517592205 0.12595878543131592 chr10 135534747 1796318 0.01325356072712483 0.16146715501328152 chr11 135006516 2107925 0.015613505647386679 0.14495396707789004 chr12 133851895 1381867 0.010323850850225169 0.11007070328624377 chr13 115169878 999968 0.0086825480530595 0.09945720223470879 chr14 107349540 762673 0.007104576321426249 0.09132915687524366 chr15 102531392 1056658 0.010305702277015804 0.10767699596073145 chr16 90354753 1226175 0.013570675136481199 0.12799043686218692 chr17 81195210 920237 0.011333636553190762 0.11574048308838512 chr18 78077248 1085548 0.013903512582820542 0.1866833674492198 chr19 59128983 849994 0.014375251473545554 0.202854910678913 chr20 63025520 780693 0.012386934689313154 0.12196281931398047 chr21 48129895 378865 0.007871718814262943 0.10782985174934001 chr22 51304566 654919 0.012765316053935629 0.11977094400309338 chrMT 16571 4266 0.2574376923541126 0.5122228665986351 chrX 155270560 1704491 0.01097755427687 0.11774654251667864 chrY 59373566 125834 0.0021193606595904984 0.0832429629940065