BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174050.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 = 2,591,860 number of mapped reads = 2,532,914 (97.73%) number of supplementary alignments = 244,634 (9.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,267,586 number of mapped paired reads (second in pair) = 1,265,328 number of mapped paired reads (both in pair) = 2,494,450 number of mapped paired reads (singletons) = 38,464 number of mapped bases = 300,402,588 bp number of sequenced bases = 300,233,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,939,614 duplication rate = 64.37% >>>>>>> Insert size mean insert size = 930,367.6808 std insert size = 9,121,437.9766 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.6799 >>>>>>> ACTG content number of A's = 90,177,355 bp (30.04%) number of C's = 59,098,031 bp (19.68%) number of T's = 89,899,869 bp (29.94%) number of G's = 61,054,482 bp (20.34%) number of N's = 3,562 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,045,562 number of insertions = 30,476 mapped reads with insertion percentage = 1.17% number of deletions = 67,107 mapped reads with deletion percentage = 2.58% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.097X std coverageData = 1.5515X There is a 2.12% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 1.02% of reference with a coverageData >= 4X There is a 0.76% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 30257255 0.12139289715149797 1.420493182535059 chr2 243199373 32767281 0.13473423305248405 4.128965878036 chr3 198022430 24157878 0.12199566483453415 1.0001123481340886 chr4 191154276 16639116 0.08704548152509024 0.889312509379369 chr5 180915260 16828754 0.09302009128472634 0.8574721090381059 chr6 171115067 16980842 0.09923639278357645 0.9207197861843115 chr7 159138663 20279207 0.12743105049211076 1.5028591125726039 chr8 146364022 8899492 0.06080382240384184 0.8000145214311514 chr9 141213431 11246366 0.07964090894441904 0.936547385268614 chr10 135534747 14412396 0.10633727748058584 1.5519507781526913 chr11 135006516 13004532 0.0963252173695083 0.8783133023108226 chr12 133851895 10524059 0.07862465451086816 0.8036707809786187 chr13 115169878 9193541 0.07982591593958274 0.8014391311293807 chr14 107349540 7517842 0.07003143189994107 0.7490871710119968 chr15 102531392 10679949 0.10416272315897164 0.9097391778874113 chr16 90354753 12562019 0.1390299744386441 1.4389054408412632 chr17 81195210 7561044 0.09312179868738563 0.901295012734058 chr18 78077248 4867072 0.062336623340002964 1.1941497331786934 chr19 59128983 5949633 0.10062126385633928 1.3752103189979956 chr20 63025520 8230535 0.13059051317624987 1.0033964050443192 chr21 48129895 4772039 0.09914916706134513 0.9042208292646708 chr22 51304566 2774719 0.05408327594078079 0.6302606657190309 chrMT 16571 1375138 82.9846116709915 66.78000383444542 chrX 155270560 8522418 0.05488753309062581 0.6561038420104056 chrY 59373566 399461 0.006727926700579177 0.3087511830263641