BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524304.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 = 997,411 number of mapped reads = 905,469 (90.78%) number of supplementary alignments = 3,241 (0.32%) number of secondary alignments = 0 number of mapped bases = 52,259,320 bp number of sequenced bases = 52,244,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,541 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5642 >>>>>>> ACTG content number of A's = 13,461,295 bp (25.77%) number of C's = 9,781,434 bp (18.72%) number of T's = 15,973,803 bp (30.57%) number of G's = 13,021,588 bp (24.92%) number of N's = 6,865 bp (0.01%) GC percentage = 43.65% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 273,462 number of insertions = 3,906 mapped reads with insertion percentage = 0.43% number of deletions = 9,020 mapped reads with deletion percentage = 0.99% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1837X There is a 1.57% of reference with a coverageData >= 1X There is a 0.08% 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 4369317 0.017529813897635183 0.30631382046574 chr2 243199373 3367395 0.013846232243370135 0.2440439860070103 chr3 198022430 3673607 0.018551469144177254 0.14306586461657006 chr4 191154276 2706837 0.01416048365038928 0.1337008501791725 chr5 180915260 3035586 0.01677904893152739 0.13633131362861314 chr6 171115067 3306095 0.019320887739242742 0.15432626973447963 chr7 159138663 2389359 0.015014321189816706 0.21487924231758876 chr8 146364022 5347421 0.03653507827217265 0.2330913052892821 chr9 141213431 2142670 0.015173273426095 0.1517210539242649 chr10 135534747 2682905 0.019794960771203563 0.17849947607294647 chr11 135006516 2509220 0.018585917734518828 0.1650470091079241 chr12 133851895 2079362 0.015534796873813404 0.13290291916231076 chr13 115169878 1313406 0.011404075638597098 0.11210943206149851 chr14 107349540 1265195 0.011785751480630472 0.11793876141110265 chr15 102531392 1594255 0.015548945244008782 0.13303596789851937 chr16 90354753 1667765 0.018457966455843224 0.14723408424569107 chr17 81195210 1648635 0.020304584469945947 0.15850207688420742 chr18 78077248 1214347 0.015553148082268473 0.2432697078156553 chr19 59128983 933875 0.01579386203885834 0.22394301092844424 chr20 63025520 1175478 0.018650825887672168 0.14489902725120837 chr21 48129895 754204 0.015670177547655154 0.13684278140851105 chr22 51304566 383930 0.007483349532671224 0.0908801421508099 chrMT 16571 1413 0.08526944662361957 0.2980954846764379 chrX 155270560 2550746 0.016427750373283898 0.1460192028743815 chrY 59373566 146297 0.0024640089833917 0.07567764905454559