BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524999.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 = 1,434,634 number of mapped reads = 1,304,140 (90.9%) number of supplementary alignments = 4,093 (0.29%) number of secondary alignments = 0 number of mapped bases = 75,087,954 bp number of sequenced bases = 75,063,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,187 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6756 >>>>>>> ACTG content number of A's = 18,917,920 bp (25.2%) number of C's = 13,874,854 bp (18.48%) number of T's = 24,274,227 bp (32.34%) number of G's = 17,996,130 bp (23.97%) number of N's = 715 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 375,926 number of insertions = 5,647 mapped reads with insertion percentage = 0.43% number of deletions = 14,802 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.96% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2349X There is a 2.22% of reference with a coverageData >= 1X There is a 0.14% 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 8168486 0.03277217913130094 0.44002110004381223 chr2 243199373 6304841 0.025924577527590913 0.2710725837188508 chr3 198022430 4185032 0.021134131118378863 0.1565345501685396 chr4 191154276 4892407 0.025594023332232443 0.18271501354900002 chr5 180915260 3317827 0.01833912186290974 0.14725047081931952 chr6 171115067 5646942 0.03300084614991852 0.26293635477083827 chr7 159138663 4836136 0.03038944722062922 0.3042499933811554 chr8 146364022 4462880 0.03049164636921497 0.22960081316505615 chr9 141213431 2106772 0.01491906247926233 0.17007791656103766 chr10 135534747 3910165 0.028849908134627646 0.2334814675152336 chr11 135006516 3242612 0.02401818887023201 0.206866343043669 chr12 133851895 3538146 0.026433290316883448 0.17586695973532762 chr13 115169878 1473897 0.012797591050673858 0.12170944285315932 chr14 107349540 1735308 0.016165025020135157 0.1396518491605115 chr15 102531392 2325845 0.022684223383995412 0.16716498468117855 chr16 90354753 2156705 0.023869303256243753 0.17247309381403914 chr17 81195210 1901436 0.023418080943444816 0.20395336084277016 chr18 78077248 1703594 0.02181933973902359 0.2922103506884176 chr19 59128983 1877221 0.03174789933390196 0.2710709345730125 chr20 63025520 1705605 0.02706213292647169 0.1778481916869885 chr21 48129895 1112909 0.02312302987571446 0.16849214777457117 chr22 51304566 1045760 0.020383370945969995 0.15186852588407374 chrMT 16571 29448 1.7770804417355621 1.6465887339156648 chrX 155270560 3203106 0.020629190749360343 0.17408303491829422 chrY 59373566 204874 0.0034505928109488993 0.10393636387116728