BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352030.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 = 1,336,675,720 number of mapped reads = 1,298,801,732 (97.17%) number of supplementary alignments = 29,274,740 (2.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 650,371,204 number of mapped paired reads (second in pair) = 648,430,528 number of mapped paired reads (both in pair) = 1,287,814,374 number of mapped paired reads (singletons) = 10,987,358 number of mapped bases = 117,487,910,158 bp number of sequenced bases = 117,412,777,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,779,823 duplication rate = 30.53% >>>>>>> Insert size mean insert size = 153,627.3823 std insert size = 3,834,024.3476 median insert size = 284 >>>>>>> Mapping quality mean mapping quality = 52.9573 >>>>>>> ACTG content number of A's = 33,959,488,488 bp (28.92%) number of C's = 24,527,098,627 bp (20.89%) number of T's = 33,666,772,840 bp (28.67%) number of G's = 25,257,061,333 bp (21.51%) number of N's = 2,356,499 bp (0%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 848,059,447 number of insertions = 15,126,461 mapped reads with insertion percentage = 1.14% number of deletions = 50,182,853 mapped reads with deletion percentage = 3.78% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 37.952X std coverageData = 319.1197X There is a 91.79% of reference with a coverageData >= 1X There is a 91.72% of reference with a coverageData >= 2X There is a 91.68% of reference with a coverageData >= 3X There is a 91.64% of reference with a coverageData >= 4X There is a 91.61% of reference with a coverageData >= 5X There is a 91.58% of reference with a coverageData >= 6X There is a 91.55% of reference with a coverageData >= 7X There is a 91.52% of reference with a coverageData >= 8X There is a 91.48% of reference with a coverageData >= 9X There is a 91.44% of reference with a coverageData >= 10X There is a 91.39% of reference with a coverageData >= 11X There is a 91.32% of reference with a coverageData >= 12X There is a 91.24% of reference with a coverageData >= 13X There is a 91.13% of reference with a coverageData >= 14X There is a 90.99% of reference with a coverageData >= 15X There is a 90.79% of reference with a coverageData >= 16X There is a 90.54% of reference with a coverageData >= 17X There is a 90.2% of reference with a coverageData >= 18X There is a 89.75% of reference with a coverageData >= 19X There is a 89.18% of reference with a coverageData >= 20X There is a 88.45% of reference with a coverageData >= 21X There is a 87.56% of reference with a coverageData >= 22X There is a 86.47% of reference with a coverageData >= 23X There is a 85.17% of reference with a coverageData >= 24X There is a 83.65% of reference with a coverageData >= 25X There is a 81.91% of reference with a coverageData >= 26X There is a 79.93% of reference with a coverageData >= 27X There is a 77.74% of reference with a coverageData >= 28X There is a 75.34% of reference with a coverageData >= 29X There is a 72.74% of reference with a coverageData >= 30X There is a 69.98% of reference with a coverageData >= 31X There is a 67.07% of reference with a coverageData >= 32X There is a 64.05% of reference with a coverageData >= 33X There is a 60.94% of reference with a coverageData >= 34X There is a 57.77% of reference with a coverageData >= 35X There is a 54.57% of reference with a coverageData >= 36X There is a 51.37% of reference with a coverageData >= 37X There is a 48.18% of reference with a coverageData >= 38X There is a 45.04% of reference with a coverageData >= 39X There is a 41.97% of reference with a coverageData >= 40X There is a 38.97% of reference with a coverageData >= 41X There is a 36.07% of reference with a coverageData >= 42X There is a 33.28% of reference with a coverageData >= 43X There is a 30.61% of reference with a coverageData >= 44X There is a 28.07% of reference with a coverageData >= 45X There is a 25.66% of reference with a coverageData >= 46X There is a 23.39% of reference with a coverageData >= 47X There is a 21.26% of reference with a coverageData >= 48X There is a 19.27% of reference with a coverageData >= 49X There is a 17.42% of reference with a coverageData >= 50X There is a 15.7% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9761110089 39.16182856370897 722.0093390142218 chr2 243199373 10044008009 41.299481512232354 359.25443320771666 chr3 198022430 7754041916 39.15739199847209 30.41958469744603 chr4 191154276 7317047252 38.27822952806978 216.39712755374975 chr5 180915260 7013591187 38.76727251753113 25.284217825439924 chr6 171115067 6577200700 38.437297283704424 83.76385412376771 chr7 159138663 6236601517 39.18973176870287 215.1144973969807 chr8 146364022 5774058410 39.44998457339468 453.5828367844898 chr9 141213431 4970759958 35.200334152351274 227.8365394646448 chr10 135534747 5989844594 44.1941622099313 663.6936423790681 chr11 135006516 5378200685 39.83660081266004 127.94638386202611 chr12 133851895 5321468995 39.75639638871007 55.5311986844527 chr13 115169878 3578277535 31.069560870768658 21.82105563066013 chr14 107349540 3572862283 33.28251134564712 34.953589861047114 chr15 102531392 3464418532 33.78885689955326 24.682734338907867 chr16 90354753 3816693937 42.24120824058918 273.6618097235998 chr17 81195210 3542854182 43.63378310124452 127.65708621788544 chr18 78077248 3067634673 39.289738708515955 380.6353445779962 chr19 59128983 2551131533 43.14519552957642 298.694389837808 chr20 63025520 2525465847 40.0705277322583 41.645267236668666 chr21 48129895 1564759522 32.51117672290787 75.75718814520827 chr22 51304566 1559624215 30.399325763714675 32.56153934373559 chrMT 16571 349166542 21070.93971395812 4035.734269999031 chrX 155270560 5403726106 34.802000495135715 62.22409291129399 chrY 59373566 353361939 5.951502710819155 213.13862188118637