BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751227.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,684,265 number of mapped reads = 4,188,570 (89.42%) number of supplementary alignments = 164,014 (3.5%) number of secondary alignments = 0 number of mapped bases = 411,574,090 bp number of sequenced bases = 411,446,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,252 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1969 >>>>>>> ACTG content number of A's = 119,888,616 bp (29.14%) number of C's = 85,840,316 bp (20.86%) number of T's = 120,530,368 bp (29.29%) number of G's = 85,185,415 bp (20.7%) number of N's = 2,222 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,598,161 number of insertions = 111,955 mapped reads with insertion percentage = 2.61% number of deletions = 57,258 mapped reads with deletion percentage = 1.34% homopolymer indels = 48.59% >>>>>>> Coverage mean coverageData = 0.133X std coverageData = 1.3677X There is a 10.44% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 49601575 0.19900281411936782 3.820543556271236 chr2 243199373 30760369 0.12648210651431244 0.5909720355992173 chr3 198022430 27076832 0.13673618690569547 0.4905132586594828 chr4 191154276 18953355 0.09915213719833293 0.48416282030302 chr5 180915260 28851562 0.15947555778324063 0.48184731829678 chr6 171115067 22700796 0.1326639225755614 0.8250245518882865 chr7 159138663 23030368 0.1447188732508077 0.7646607718508677 chr8 146364022 20377044 0.1392216729327102 0.5355849018429781 chr9 141213431 18024737 0.12764180342024264 0.6446100534913733 chr10 135534747 21007309 0.15499574437542574 1.9307072200496975 chr11 135006516 18895983 0.1399634888733815 0.754317447220251 chr12 133851895 21735003 0.16238098833042297 0.49265020374259044 chr13 115169878 11577853 0.100528481935181 0.370177864884275 chr14 107349540 8750560 0.08151464831614555 0.35638421815809357 chr15 102531392 11163345 0.10887733778158401 0.3845603225457313 chr16 90354753 12722889 0.140810400975807 1.0283836436206013 chr17 81195210 12117587 0.14924017069479836 0.6610707602543497 chr18 78077248 8890961 0.11387390344495749 1.317043602639087 chr19 59128983 7356556 0.1244153987901331 2.684767043177815 chr20 63025520 8166626 0.12957649536251348 0.4394950773502587 chr21 48129895 5383942 0.1118627414416757 0.44802719248858053 chr22 51304566 4831922 0.09418112999922854 0.3624130241360083 chrMT 16571 1587160 95.77937360448978 38.05563669261623 chrX 155270560 16941575 0.1091100270392533 0.46329582174189027 chrY 59373566 1068181 0.017990851349571964 0.7202592687508568