BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174088.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,279,740 number of mapped reads = 4,185,661 (97.8%) number of supplementary alignments = 535,969 (12.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,095,482 number of mapped paired reads (second in pair) = 2,090,179 number of mapped paired reads (both in pair) = 4,127,580 number of mapped paired reads (singletons) = 58,081 number of mapped bases = 473,393,662 bp number of sequenced bases = 473,049,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,337,816 duplication rate = 63.83% >>>>>>> Insert size mean insert size = 1,176,744.7221 std insert size = 10,096,198.8442 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.6746 >>>>>>> ACTG content number of A's = 141,741,654 bp (29.96%) number of C's = 93,627,368 bp (19.79%) number of T's = 140,493,259 bp (29.7%) number of G's = 97,183,211 bp (20.54%) number of N's = 4,053 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 4,056,901 number of insertions = 52,377 mapped reads with insertion percentage = 1.2% number of deletions = 144,982 mapped reads with deletion percentage = 3.38% homopolymer indels = 40.67% >>>>>>> Coverage mean coverageData = 0.1529X std coverageData = 2.845X There is a 3.28% of reference with a coverageData >= 1X There is a 2.43% of reference with a coverageData >= 2X There is a 1.79% of reference with a coverageData >= 3X There is a 1.45% of reference with a coverageData >= 4X There is a 1.09% of reference with a coverageData >= 5X There is a 0.91% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.6% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 38252811 0.15347127660717041 1.7361614050573473 chr2 243199373 44055617 0.18115020798182732 8.92264898318494 chr3 198022430 32783451 0.1655542303970313 1.2504404366214559 chr4 191154276 32273396 0.16883428754688176 1.5712525758860194 chr5 180915260 30380625 0.16792737660714746 1.2559587832568313 chr6 171115067 28554756 0.1668745862104592 1.3696854838644226 chr7 159138663 25483070 0.160131230963025 1.509887682128032 chr8 146364022 24341508 0.16630800156612258 1.6956018173881353 chr9 141213431 20770404 0.14708518766886983 1.4436401685389577 chr10 135534747 22561211 0.1664607157897303 1.8889521515085754 chr11 135006516 22223525 0.16461075849109386 1.2768766101167444 chr12 133851895 21354516 0.15953839129434813 1.2418950082335949 chr13 115169878 15387351 0.1336056898488683 1.1188037651226768 chr14 107349540 14292507 0.13313989980767502 1.1195330905965637 chr15 102531392 13243764 0.12916789425817998 1.1074750128699897 chr16 90354753 14443325 0.15985130300782296 1.4323301067532843 chr17 81195210 12501284 0.15396578197162122 1.2074363250744689 chr18 78077248 13107792 0.16788235159108067 1.813919000032266 chr19 59128983 8687266 0.1469206057543726 1.2852543340659142 chr20 63025520 9760450 0.154865045143618 1.2298172619786014 chr21 48129895 6546007 0.13600709081123075 1.432998222895971 chr22 51304566 5395580 0.10516763751592792 1.1472759791672942 chrMT 16571 677577 40.88932472391527 34.84507708258972 chrX 155270560 12791212 0.08238014984939837 0.877890791852123 chrY 59373566 3524657 0.059364077946741485 1.1099816600808499