BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173885.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 = 1,267,908 number of mapped reads = 1,231,314 (97.11%) number of supplementary alignments = 128,363 (10.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 616,768 number of mapped paired reads (second in pair) = 614,546 number of mapped paired reads (both in pair) = 1,209,388 number of mapped paired reads (singletons) = 21,926 number of mapped bases = 144,556,748 bp number of sequenced bases = 144,465,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 886,888 duplication rate = 60.36% >>>>>>> Insert size mean insert size = 1,125,268.134 std insert size = 9,560,510.8455 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.6665 >>>>>>> ACTG content number of A's = 43,895,617 bp (30.38%) number of C's = 27,976,687 bp (19.37%) number of T's = 43,610,142 bp (30.19%) number of G's = 28,981,095 bp (20.06%) number of N's = 1,748 bp (0%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 1,580,730 number of insertions = 18,043 mapped reads with insertion percentage = 1.41% number of deletions = 36,359 mapped reads with deletion percentage = 2.87% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 0.8647X There is a 1.2% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 11710002 0.046980833801011875 0.6699776950762251 chr2 243199373 13289294 0.054643619496502566 2.178000009983053 chr3 198022430 10044861 0.05072587484155204 0.5983715270762202 chr4 191154276 9938241 0.051990681076891004 0.7227032006530211 chr5 180915260 9307895 0.05144892144532197 0.6062343742120814 chr6 171115067 8255354 0.048244459969150465 0.6027493458206651 chr7 159138663 7756534 0.04874072619298052 0.6513275818226766 chr8 146364022 7515479 0.051347857877258936 0.8071256282487146 chr9 141213431 5879399 0.0416348427933884 0.6767807299063071 chr10 135534747 7038598 0.051932055475043606 0.8190002283152212 chr11 135006516 6511504 0.048231035011673064 0.5841546788935679 chr12 133851895 6487663 0.04846896639005372 0.5732881689952728 chr13 115169878 5153296 0.04474517199714321 0.5636214338065408 chr14 107349540 4696980 0.04375407663600608 0.5562045114753608 chr15 102531392 4057604 0.03957426033970162 0.5200060486406863 chr16 90354753 4538956 0.05023483380005477 0.6533362284018697 chr17 81195210 3861070 0.047552928306977715 0.5984207878644958 chr18 78077248 4143353 0.05306735452561033 0.8861920512611707 chr19 59128983 2455006 0.041519503218920575 0.5767239465748185 chr20 63025520 2888718 0.04583410021845119 0.5634634556489475 chr21 48129895 2128794 0.04423018167814411 0.6364160154568698 chr22 51304566 1764336 0.03438945375739071 0.49404844660699393 chrMT 16571 185125 11.171625128236075 10.589324416726813 chrX 155270560 3640314 0.023444972440364743 0.4011515160788231 chrY 59373566 1308372 0.022036271158111003 0.4824599390916726