BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971287.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,680,103 number of mapped reads = 9,218,688 (86.32%) number of secondary alignments = 0 number of mapped bases = 362,687,239 bp number of sequenced bases = 362,652,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 880,994 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.2553 >>>>>>> ACTG content number of A's = 101,745,450 bp (28.06%) number of C's = 77,098,885 bp (21.26%) number of T's = 105,021,534 bp (28.96%) number of G's = 78,784,061 bp (21.72%) number of N's = 2,642 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,415,497 number of insertions = 15,312 mapped reads with insertion percentage = 0.17% number of deletions = 28,707 mapped reads with deletion percentage = 0.31% homopolymer indels = 36.62% >>>>>>> Coverage mean coverageData = 0.1172X std coverageData = 1.8765X There is a 8.94% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% 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 29119707 0.11682902487131616 4.25375686720482 chr2 243199373 30690825 0.1261961518297171 1.583850816271234 chr3 198022430 24131357 0.12186173556197649 0.4623916730403996 chr4 191154276 24166706 0.1264251394512357 0.5394458240750072 chr5 180915260 22341202 0.12348987034040136 0.5693095446101148 chr6 171115067 20812142 0.12162658943411453 0.5513088938165437 chr7 159138663 21201640 0.13322746088422271 2.6697493156357726 chr8 146364022 18917242 0.12924789672697024 2.8121056971289384 chr9 141213431 15346870 0.10867854347367284 1.605950776246735 chr10 135534747 17292820 0.127589569337522 1.4262755131638494 chr11 135006516 16688495 0.12361251511741848 1.1811252159935053 chr12 133851895 16434072 0.12277803015041364 0.6228624849180054 chr13 115169878 8495827 0.07376778674715623 0.32723707403264146 chr14 107349540 10907613 0.10160838136800586 0.9133038100435361 chr15 102531392 9736278 0.09495899558254314 0.39632145519568607 chr16 90354753 9735624 0.10774888621520552 0.7210012172445533 chr17 81195210 9326090 0.1148601007374696 0.6167016088400118 chr18 78077248 9698808 0.12422066925309662 3.5401321106597137 chr19 59128983 8407102 0.1421824217744452 4.143027709717985 chr20 63025520 6848565 0.10866336366601974 0.6127329721810497 chr21 48129895 4358709 0.09056136523879804 0.6795909366823126 chr22 51304566 3798544 0.07403910209473363 0.3390945779530942 chrMT 16571 15940 0.9619214290024742 1.3481491986484062 chrX 155270560 22270914 0.14343294697977518 0.9792420753716341 chrY 59373566 1944147 0.03274431924806403 0.3997825699812473