BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525274.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 = 1,183,405 number of mapped reads = 1,075,871 (90.91%) number of supplementary alignments = 4,494 (0.38%) number of secondary alignments = 0 number of mapped bases = 62,307,372 bp number of sequenced bases = 62,285,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,271 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0821 >>>>>>> ACTG content number of A's = 16,013,733 bp (25.71%) number of C's = 11,819,045 bp (18.98%) number of T's = 19,948,185 bp (32.03%) number of G's = 14,503,729 bp (23.29%) number of N's = 1,218 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 315,857 number of insertions = 4,395 mapped reads with insertion percentage = 0.41% number of deletions = 13,444 mapped reads with deletion percentage = 1.24% homopolymer indels = 43.6% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2172X There is a 1.86% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6309216 0.025312739341179013 0.38522295967700715 chr2 243199373 4855742 0.019966095882985684 0.27734778172443736 chr3 198022430 4394317 0.02219100634205933 0.1580766594214437 chr4 191154276 3408184 0.017829493910981098 0.14577586434147696 chr5 180915260 2711115 0.01498555179922357 0.1301779058813778 chr6 171115067 3753422 0.021935076003564313 0.17018588610582047 chr7 159138663 4380060 0.0275235440428452 0.35293704906090656 chr8 146364022 4300296 0.02938082693573425 0.23347822559327985 chr9 141213431 1994297 0.014122573085841954 0.15163406276080113 chr10 135534747 3735706 0.027562717920593456 0.22240019009289425 chr11 135006516 2756134 0.020414822051996365 0.18050126925886947 chr12 133851895 2692834 0.02011801177712127 0.15093054452149304 chr13 115169878 1895360 0.016457080904435793 0.13664811105612845 chr14 107349540 2236807 0.020836670562351733 0.15430250248384283 chr15 102531392 1630154 0.015899072159285616 0.1369707923173226 chr16 90354753 1529289 0.016925385209121208 0.14640144354466653 chr17 81195210 1081664 0.01332177107491932 0.12527074057553123 chr18 78077248 1283956 0.01644468821442067 0.2656658291384258 chr19 59128983 1126000 0.01904311460929406 0.2526402222128612 chr20 63025520 1079799 0.01713272655267263 0.13875760071955506 chr21 48129895 856026 0.01778574418248783 0.14709459862115595 chr22 51304566 647843 0.012627394606554123 0.11840598048349242 chrMT 16571 124611 7.5198237885462555 5.0201998007791495 chrX 155270560 3347827 0.0215612476698738 0.16281076065492864 chrY 59373566 176713 0.0029762908294913596 0.08663578402055251