BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237854.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,532,376 number of mapped reads = 3,350,969 (94.86%) number of supplementary alignments = 34,340 (0.97%) number of secondary alignments = 0 number of mapped bases = 245,817,138 bp number of sequenced bases = 245,695,132 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,733 duplication rate = 6.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0114 >>>>>>> ACTG content number of A's = 75,241,693 bp (30.62%) number of C's = 48,199,093 bp (19.62%) number of T's = 74,001,747 bp (30.12%) number of G's = 47,819,150 bp (19.46%) number of N's = 433,449 bp (0.18%) GC percentage = 39.08% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 2,260,324 number of insertions = 19,651 mapped reads with insertion percentage = 0.58% number of deletions = 67,688 mapped reads with deletion percentage = 2% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.0794X std coverageData = 1.5432X There is a 2.27% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 25703595 0.10312349432421274 3.907925733625117 chr2 243199373 32912082 0.1353296334361849 1.5284543864970608 chr3 198022430 10851179 0.05479772670197008 0.6892283851102993 chr4 191154276 16358335 0.08557661038144918 0.81256369645429 chr5 180915260 10973410 0.06065497183598553 0.6389741080110923 chr6 171115067 13002214 0.07598520824586417 0.7560026300196102 chr7 159138663 14533668 0.09132707115931972 1.4283788427493769 chr8 146364022 8491457 0.05801601297892729 1.0289065758229563 chr9 141213431 9052688 0.06410642341803875 1.2446911674747845 chr10 135534747 6883573 0.050788252845596855 1.580341216920146 chr11 135006516 10859597 0.08043757680555211 1.0229909299248423 chr12 133851895 14147546 0.1056955226521074 0.8552584198057847 chr13 115169878 2828010 0.02455511848332426 0.3766836260395626 chr14 107349540 3800135 0.03539963934638192 0.558727578630327 chr15 102531392 3622665 0.035332252194527895 0.46782165926704006 chr16 90354753 5519185 0.06108350492640935 0.8760847071707487 chr17 81195210 7840563 0.09656435398097991 1.0849769827059577 chr18 78077248 12419433 0.15906596759148067 2.5446329936104344 chr19 59128983 4745487 0.08025653003367232 2.2203080053522433 chr20 63025520 2344002 0.03719131551790449 0.5108194904481412 chr21 48129895 2022649 0.0420247956078026 0.5690952658988787 chr22 51304566 2616439 0.050998170416254957 0.5809077900552364 chrMT 16571 35162 2.1218997043026975 3.1167651220145522 chrX 155270560 23558740 0.1517270241055355 1.2239277834964066 chrY 59373566 695324 0.011711002839209624 0.38829929117028816