BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173937.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 = 6,703,104 number of mapped reads = 6,564,541 (97.93%) number of supplementary alignments = 843,934 (12.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,285,972 number of mapped paired reads (second in pair) = 3,278,569 number of mapped paired reads (both in pair) = 6,477,156 number of mapped paired reads (singletons) = 87,385 number of mapped bases = 744,360,945 bp number of sequenced bases = 743,850,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,378,803 duplication rate = 66.81% >>>>>>> Insert size mean insert size = 1,231,947.6438 std insert size = 10,676,355.0812 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 52.6534 >>>>>>> ACTG content number of A's = 221,803,432 bp (29.82%) number of C's = 148,205,188 bp (19.92%) number of T's = 219,963,107 bp (29.57%) number of G's = 153,873,493 bp (20.69%) number of N's = 5,642 bp (0%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 6,218,297 number of insertions = 81,379 mapped reads with insertion percentage = 1.2% number of deletions = 216,847 mapped reads with deletion percentage = 3.23% homopolymer indels = 41.41% >>>>>>> Coverage mean coverageData = 0.2405X std coverageData = 4.4118X There is a 4.79% of reference with a coverageData >= 1X There is a 3.7% of reference with a coverageData >= 2X There is a 2.82% of reference with a coverageData >= 3X There is a 2.31% of reference with a coverageData >= 4X There is a 1.77% of reference with a coverageData >= 5X There is a 1.48% of reference with a coverageData >= 6X There is a 1.13% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.51% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 67545767 0.27099538099044496 2.301204132137559 chr2 243199373 61925179 0.2546272148489462 14.366035180429458 chr3 198022430 48861337 0.24674647715412845 1.553569073497902 chr4 191154276 43403594 0.22706054454151997 1.911408454731476 chr5 180915260 42902303 0.23714032193856946 1.5302147697947088 chr6 171115067 43368009 0.25344354392825036 1.883189667213993 chr7 159138663 43111960 0.27090814505586236 2.234091460226276 chr8 146364022 42606895 0.29110224232564474 2.3692398177906884 chr9 141213431 33031373 0.23391098683807207 2.136380554026726 chr10 135534747 40110351 0.2959414606794522 2.4644887058656435 chr11 135006516 32720475 0.2423621908738094 1.6120303891568968 chr12 133851895 34158160 0.25519369748183246 1.6292235141043638 chr13 115169878 23465912 0.20375042856257952 1.4130056633804668 chr14 107349540 21604194 0.20125092291965108 1.4393351986352063 chr15 102531392 21765439 0.21228073251946097 1.4670848914047048 chr16 90354753 22201265 0.24571219844959347 1.7564678763774941 chr17 81195210 23090704 0.2843850517783007 1.8073149338721257 chr18 78077248 21406570 0.27417167674762305 2.6910572103416857 chr19 59128983 15414652 0.2606953682934137 1.941435073929658 chr20 63025520 16663987 0.2644006269206506 1.6165895354257935 chr21 48129895 9093552 0.18893770701141152 1.700849911210814 chr22 51304566 9866458 0.19231149913635368 1.4430703786090149 chrMT 16571 406847 24.551747027940376 22.89453645605609 chrX 155270560 20418079 0.13150000231853354 1.126636620589792 chrY 59373566 5217883 0.08788225723211572 1.3552819963975427