BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328244.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,032,170,794 number of mapped reads = 1,014,283,850 (98.27%) number of supplementary alignments = 44,943,857 (4.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 508,593,780 number of mapped paired reads (second in pair) = 505,690,070 number of mapped paired reads (both in pair) = 1,007,168,312 number of mapped paired reads (singletons) = 7,115,538 number of mapped bases = 141,539,366,098 bp number of sequenced bases = 141,323,497,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 391,238,973 duplication rate = 33.71% >>>>>>> Insert size mean insert size = 169,141.9308 std insert size = 3,993,354.4511 median insert size = 274 >>>>>>> Mapping quality mean mapping quality = 53.7549 >>>>>>> ACTG content number of A's = 40,394,942,663 bp (28.58%) number of C's = 29,888,362,582 bp (21.15%) number of T's = 39,964,883,828 bp (28.28%) number of G's = 31,072,683,864 bp (21.99%) number of N's = 2,624,229 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,198,894,398 number of insertions = 20,872,132 mapped reads with insertion percentage = 1.95% number of deletions = 91,153,462 mapped reads with deletion percentage = 8.57% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 45.7214X std coverageData = 925.6419X There is a 91.73% of reference with a coverageData >= 1X There is a 91.65% of reference with a coverageData >= 2X There is a 91.59% of reference with a coverageData >= 3X There is a 91.55% of reference with a coverageData >= 4X There is a 91.51% of reference with a coverageData >= 5X There is a 91.47% of reference with a coverageData >= 6X There is a 91.43% of reference with a coverageData >= 7X There is a 91.39% of reference with a coverageData >= 8X There is a 91.34% of reference with a coverageData >= 9X There is a 91.29% of reference with a coverageData >= 10X There is a 91.24% of reference with a coverageData >= 11X There is a 91.18% of reference with a coverageData >= 12X There is a 91.1% of reference with a coverageData >= 13X There is a 91.01% of reference with a coverageData >= 14X There is a 90.91% of reference with a coverageData >= 15X There is a 90.78% of reference with a coverageData >= 16X There is a 90.62% of reference with a coverageData >= 17X There is a 90.43% of reference with a coverageData >= 18X There is a 90.19% of reference with a coverageData >= 19X There is a 89.89% of reference with a coverageData >= 20X There is a 89.54% of reference with a coverageData >= 21X There is a 89.1% of reference with a coverageData >= 22X There is a 88.58% of reference with a coverageData >= 23X There is a 87.95% of reference with a coverageData >= 24X There is a 87.21% of reference with a coverageData >= 25X There is a 86.35% of reference with a coverageData >= 26X There is a 85.36% of reference with a coverageData >= 27X There is a 84.22% of reference with a coverageData >= 28X There is a 82.94% of reference with a coverageData >= 29X There is a 81.5% of reference with a coverageData >= 30X There is a 79.92% of reference with a coverageData >= 31X There is a 78.18% of reference with a coverageData >= 32X There is a 76.29% of reference with a coverageData >= 33X There is a 74.27% of reference with a coverageData >= 34X There is a 72.12% of reference with a coverageData >= 35X There is a 69.85% of reference with a coverageData >= 36X There is a 67.48% of reference with a coverageData >= 37X There is a 65.02% of reference with a coverageData >= 38X There is a 62.48% of reference with a coverageData >= 39X There is a 59.9% of reference with a coverageData >= 40X There is a 57.28% of reference with a coverageData >= 41X There is a 54.64% of reference with a coverageData >= 42X There is a 52.01% of reference with a coverageData >= 43X There is a 49.38% of reference with a coverageData >= 44X There is a 46.79% of reference with a coverageData >= 45X There is a 44.25% of reference with a coverageData >= 46X There is a 41.75% of reference with a coverageData >= 47X There is a 39.33% of reference with a coverageData >= 48X There is a 36.99% of reference with a coverageData >= 49X There is a 34.72% of reference with a coverageData >= 50X There is a 32.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10888980515 43.68687416429747 944.8558456274159 chr2 243199373 11690416415 48.069270371844254 2945.40317942408 chr3 198022430 8574873294 43.30253544510084 41.19818106978674 chr4 191154276 8445001507 44.17898298544993 385.218291417436 chr5 180915260 7820790168 43.22902428462917 27.787414998555818 chr6 171115067 7439567870 43.47698890828825 136.21275993083634 chr7 159138663 8555620140 53.762046122003674 223.8058129318543 chr8 146364022 10411719808 71.13578641614535 669.4819736455405 chr9 141213431 7121731408 50.4323941254568 526.4034510810804 chr10 135534747 7607142932 56.12688332977816 869.4868577707892 chr11 135006516 5998092337 44.42816920777364 186.2769511143797 chr12 133851895 6354316271 47.47274045690575 65.95372826284638 chr13 115169878 4065753855 35.302232889401864 23.237896682085562 chr14 107349540 3942179363 36.72283423850722 45.46679044863578 chr15 102531392 3746481805 36.53985118040727 27.213287862376248 chr16 90354753 4080452980 45.16035786186035 88.14050796536935 chr17 81195210 3865477837 47.607215216267065 170.0225102416635 chr18 78077248 3469707141 44.439413912232155 530.638344972368 chr19 59128983 2928222812 49.522631092775605 526.1350677349038 chr20 63025520 4030703118 63.95350832488173 113.02186415190327 chr21 48129895 1723727322 35.81406778468975 170.03890010875622 chr22 51304566 1753901049 34.186061509613005 32.16976101100267 chrMT 16571 442271539 26689.49001267274 4122.908126799962 chrX 155270560 6166217745 39.712729476856396 83.98716262898171 chrY 59373566 416016867 7.006769089799996 414.0645843333379