BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524798.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 = 1,448,181 number of mapped reads = 1,300,101 (89.77%) number of supplementary alignments = 4,043 (0.28%) number of secondary alignments = 0 number of mapped bases = 73,527,492 bp number of sequenced bases = 73,504,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,067 duplication rate = 2.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3248 >>>>>>> ACTG content number of A's = 17,384,748 bp (23.65%) number of C's = 14,646,537 bp (19.93%) number of T's = 24,049,470 bp (32.72%) number of G's = 17,415,211 bp (23.69%) number of N's = 8,477 bp (0.01%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 376,914 number of insertions = 6,165 mapped reads with insertion percentage = 0.47% number of deletions = 14,446 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.18% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2196X There is a 2.15% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5835251 0.023411179384784764 0.2831439317040505 chr2 243199373 6225469 0.025598211554599692 0.36331543699117735 chr3 198022430 4797795 0.024228543200888908 0.1722195717070424 chr4 191154276 4700643 0.024590833636386977 0.19150626494821987 chr5 180915260 4322678 0.02389338522355715 0.16759739433560472 chr6 171115067 4190612 0.02449002342967262 0.18561802556926985 chr7 159138663 4045140 0.025418964340551235 0.2601590053227675 chr8 146364022 3686459 0.02518692059446139 0.19836754336976828 chr9 141213431 3141675 0.022247706735487503 0.1890258382901231 chr10 135534747 3540291 0.02612091052931246 0.2458346000035696 chr11 135006516 3313954 0.024546622623755433 0.19796112750306802 chr12 133851895 3292288 0.024596498988677 0.17262328704811655 chr13 115169878 2307620 0.020036662711407926 0.15403100863242644 chr14 107349540 2248514 0.020945725524301267 0.16001546432116545 chr15 102531392 2154355 0.021011662457484242 0.15976296416064406 chr16 90354753 2248872 0.024889360275269636 0.18790409197283228 chr17 81195210 2093939 0.025788947402192813 0.18140351294857984 chr18 78077248 1929460 0.024712192724825548 0.273429455839988 chr19 59128983 1625269 0.027486841774363006 0.23987809967667917 chr20 63025520 1597507 0.02534698642708541 0.17862559535461778 chr21 48129895 973691 0.02023048253066 0.17076131305298498 chr22 51304566 919498 0.0179223424285472 0.14657486196400704 chrMT 16571 13389 0.8079777925291172 1.0528718306955072 chrX 155270560 4071437 0.026221564474295706 0.19094579573475873 chrY 59373566 251686 0.004239024484397652 0.1195241113062279