BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927045.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 = 19,059,932 number of mapped reads = 18,411,488 (96.6%) number of supplementary alignments = 760,728 (3.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,239,522 number of mapped paired reads (second in pair) = 9,171,966 number of mapped paired reads (both in pair) = 18,036,976 number of mapped paired reads (singletons) = 374,512 number of mapped bases = 1,644,411,743 bp number of sequenced bases = 1,643,207,662 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,533,731 duplication rate = 6.72% >>>>>>> Insert size mean insert size = 383,212.3394 std insert size = 6,045,617.6951 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.3201 >>>>>>> ACTG content number of A's = 471,080,071 bp (28.67%) number of C's = 315,802,736 bp (19.22%) number of T's = 486,045,399 bp (29.58%) number of G's = 370,088,045 bp (22.52%) number of N's = 191,411 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 17,623,236 number of insertions = 279,460 mapped reads with insertion percentage = 1.49% number of deletions = 812,288 mapped reads with deletion percentage = 4.3% homopolymer indels = 51.21% >>>>>>> Coverage mean coverageData = 0.5312X std coverageData = 2.1145X There is a 27.44% of reference with a coverageData >= 1X There is a 12.36% of reference with a coverageData >= 2X There is a 5.65% of reference with a coverageData >= 3X There is a 2.9% of reference with a coverageData >= 4X There is a 1.56% of reference with a coverageData >= 5X There is a 0.89% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 138174437 0.5543594493190851 3.1026660418855787 chr2 243199373 149524814 0.6148240110799956 3.239719560533133 chr3 198022430 110367083 0.5573463723276196 1.2048936081323098 chr4 191154276 101488436 0.5309242258331694 1.8098163321747271 chr5 180915260 97779343 0.5404704003410216 1.1569055225367237 chr6 171115067 97483592 0.5696961331873832 1.2531459097570372 chr7 159138663 83379547 0.5239427391695505 1.7105883519469327 chr8 146364022 86382414 0.5901888511918592 1.439940969796059 chr9 141213431 73433381 0.5200169734562996 2.6392194862544245 chr10 135534747 76703666 0.5659335904467362 3.9885896089135797 chr11 135006516 77643649 0.5751103820796324 2.0174506699410326 chr12 133851895 75460153 0.5637585706201619 1.210898704592652 chr13 115169878 49145149 0.4267187727679975 1.0237000748915528 chr14 107349540 50715076 0.47242937417337794 1.1728956755640993 chr15 102531392 47298358 0.4613061139363055 1.1195968778480945 chr16 90354753 46877045 0.5188110580082046 2.9660196151499085 chr17 81195210 41682331 0.5133594826591371 1.5617633977023464 chr18 78077248 42119265 0.5394563215137911 2.516489458736642 chr19 59128983 25488184 0.4310607540806173 1.7753512220499028 chr20 63025520 37077534 0.5882939799624025 1.3134872860271136 chr21 48129895 20624820 0.42852410128881435 1.5188483776942074 chr22 51304566 17290883 0.3370242523833064 0.997603163879779 chrMT 16571 78428 4.732846539134632 2.359729608451994 chrX 155270560 94238582 0.6069314234456293 1.396542836252201 chrY 59373566 3955573 0.06662178586342615 1.5542526820632128