BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926901.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,285,914 number of mapped reads = 30,390,101 (97.14%) number of supplementary alignments = 1,002,670 (3.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,232,488 number of mapped paired reads (second in pair) = 15,157,613 number of mapped paired reads (both in pair) = 29,989,934 number of mapped paired reads (singletons) = 400,167 number of mapped bases = 2,814,394,437 bp number of sequenced bases = 2,812,254,177 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,710,569 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 296,897.1603 std insert size = 5,358,211.7627 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.5925 >>>>>>> ACTG content number of A's = 801,553,007 bp (28.5%) number of C's = 563,951,683 bp (20.05%) number of T's = 807,233,076 bp (28.7%) number of G's = 639,334,160 bp (22.73%) number of N's = 182,251 bp (0.01%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 26,015,235 number of insertions = 461,543 mapped reads with insertion percentage = 1.49% number of deletions = 1,487,408 mapped reads with deletion percentage = 4.77% homopolymer indels = 52.4% >>>>>>> Coverage mean coverageData = 0.9091X std coverageData = 3.2476X There is a 34.6% of reference with a coverageData >= 1X There is a 20.11% of reference with a coverageData >= 2X There is a 11.75% of reference with a coverageData >= 3X There is a 7.42% of reference with a coverageData >= 4X There is a 4.82% of reference with a coverageData >= 5X There is a 3.23% of reference with a coverageData >= 6X There is a 2.21% of reference with a coverageData >= 7X There is a 1.54% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 0.78% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 231699076 0.9295827431459037 2.9360280804188235 chr2 243199373 241510524 0.9930557016690993 5.219589167299354 chr3 198022430 190414010 0.9615779889177201 1.9867226327276495 chr4 191154276 167852475 0.8780995042977746 2.144789719414008 chr5 180915260 169516601 0.9369944857056282 1.8873378867505735 chr6 171115067 160927879 0.9404658620739692 1.9104523316351847 chr7 159138663 145924950 0.9169672991408756 2.3885637969278264 chr8 146364022 143615464 0.9812210817765038 2.1479599857009073 chr9 141213431 119837481 0.8486266508176549 3.2809086722959964 chr10 135534747 140848716 1.0392074292210838 8.569799551313231 chr11 135006516 133882841 0.9916768832105852 2.4883250865993745 chr12 133851895 125905842 0.9406354837187774 2.1351810563173683 chr13 115169878 83991630 0.7292847006402142 1.7328788945868852 chr14 107349540 84816508 0.790096613362293 1.8215598727507083 chr15 102531392 84286421 0.8220547810372066 1.9097531340525593 chr16 90354753 89863056 0.9945581501395948 4.8303458216661515 chr17 81195210 74512161 0.9176915855011644 2.1878018862821977 chr18 78077248 73791798 0.9451126914719126 3.3008411452722997 chr19 59128983 47771755 0.8079245164761247 2.1212702270958514 chr20 63025520 66747543 1.0590558078695742 2.1985414875291265 chr21 48129895 36188335 0.7518889247524849 2.6674941921895496 chr22 51304566 37304722 0.7271228451674262 1.8727902823374876 chrMT 16571 603069 36.393036026793794 25.55993592456848 chrX 155270560 158360010 1.0198972039516054 2.121498334017376 chrY 59373566 4221570 0.07110184353757698 1.4946804013907902