BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716279.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 = 644,866 number of mapped reads = 542,990 (84.2%) number of supplementary alignments = 1,654 (0.26%) number of secondary alignments = 0 number of mapped bases = 30,038,708 bp number of sequenced bases = 30,030,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,507 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.3005 >>>>>>> ACTG content number of A's = 7,075,959 bp (23.56%) number of C's = 6,318,667 bp (21.04%) number of T's = 8,988,767 bp (29.93%) number of G's = 7,646,076 bp (25.46%) number of N's = 874 bp (0%) GC percentage = 46.5% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 158,304 number of insertions = 2,647 mapped reads with insertion percentage = 0.48% number of deletions = 4,994 mapped reads with deletion percentage = 0.91% homopolymer indels = 36.38% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.1139X There is a 0.91% of reference with a coverageData >= 1X There is a 0.04% 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 3009709 0.012075031098919508 0.13070063670268167 chr2 243199373 2627056 0.010802067322764028 0.1395888212795373 chr3 198022430 1951660 0.009855752199384686 0.10720183049451379 chr4 191154276 1885257 0.0098624892911106 0.11145464752654612 chr5 180915260 1810722 0.010008674779562542 0.1043351406237292 chr6 171115067 1282254 0.007493518966392363 0.09232586620828885 chr7 159138663 1749489 0.010993488112942108 0.12387722083560933 chr8 146364022 1845914 0.0126118015532533 0.1217372763846046 chr9 141213431 1278351 0.009052616248662637 0.10400236122355674 chr10 135534747 1541652 0.011374588687578397 0.15172767322217506 chr11 135006516 1221235 0.009045748577053866 0.11710001760801302 chr12 133851895 1462592 0.010926942797485236 0.10971236093643551 chr13 115169878 522763 0.004539060117785312 0.0708257103973835 chr14 107349540 991005 0.009231571928487071 0.10247023343690202 chr15 102531392 661485 0.006451536325577244 0.08452992095787347 chr16 90354753 816617 0.009037897541482959 0.10394269491253567 chr17 81195210 1178238 0.014511176213473677 0.12934998761080232 chr18 78077248 785653 0.010062508863017303 0.12156743225048432 chr19 59128983 827212 0.013989958190216124 0.14097003845300474 chr20 63025520 796151 0.012632200416593152 0.1202354977593042 chr21 48129895 401734 0.008346870484550194 0.10041836856000558 chr22 51304566 336327 0.0065554983936517465 0.08581226768448749 chrMT 16571 19829 1.1966085329793013 1.4426758834325288 chrX 155270560 939401 0.006050090886514482 0.08748503138286656 chrY 59373566 96402 0.001623651845334673 0.05928496802230073