BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971298.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 = 10,008,842 number of mapped reads = 8,481,521 (84.74%) number of secondary alignments = 0 number of mapped bases = 334,313,814 bp number of sequenced bases = 334,280,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 588,737 duplication rate = 5.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3298 >>>>>>> ACTG content number of A's = 96,783,062 bp (28.95%) number of C's = 67,690,465 bp (20.25%) number of T's = 99,886,168 bp (29.88%) number of G's = 69,918,439 bp (20.92%) number of N's = 2,516 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,031,800 number of insertions = 12,015 mapped reads with insertion percentage = 0.14% number of deletions = 26,570 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.24% >>>>>>> Coverage mean coverageData = 0.108X std coverageData = 0.9539X There is a 8.56% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 30211575 0.1212096277986806 2.1274926451779868 chr2 243199373 28448339 0.1169753797021508 0.7730189901051736 chr3 198022430 23266113 0.11749231135078991 0.42233465137920373 chr4 191154276 22708271 0.11879551676887416 0.454533450841873 chr5 180915260 21234270 0.11737135938670956 0.4422190613845075 chr6 171115067 20063691 0.11725262626931619 0.5337724503017236 chr7 159138663 18747970 0.11780902042641894 1.1550464846918276 chr8 146364022 17462980 0.11931197135317859 1.4851761434766655 chr9 141213431 14007273 0.09919221493881838 0.7608178900725351 chr10 135534747 15780854 0.11643400935407361 0.9416936742774478 chr11 135006516 15357013 0.11375016151072294 0.7060298834037181 chr12 133851895 15335927 0.11457385044866193 0.4454931576281525 chr13 115169878 11054130 0.09598108630452834 0.3649163621676262 chr14 107349540 10224115 0.09524134896153258 0.48702639347389864 chr15 102531392 9044289 0.08820995037305257 0.3542846792421502 chr16 90354753 8680264 0.09606870376813492 0.47312023990973323 chr17 81195210 8037508 0.09898992810043844 0.42800468304806727 chr18 78077248 8904100 0.11404218550325954 1.50249444344566 chr19 59128983 6161582 0.10420578348185018 1.8802203798241293 chr20 63025520 6319204 0.10026421043412256 0.4252868121653561 chr21 48129895 4238768 0.08806933819406837 0.456148935427772 chr22 51304566 3166637 0.061722323116425934 0.34900925681792305 chrMT 16571 35301 2.1302878522720414 2.419567364090796 chrX 155270560 12655478 0.08150597254238022 0.48981463573598166 chrY 59373566 3168162 0.053359806618319 0.4773631081190477