BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004068.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,519,148 number of mapped reads = 3,016,425 (85.71%) number of supplementary alignments = 34,225 (0.97%) number of secondary alignments = 0 number of mapped bases = 196,080,086 bp number of sequenced bases = 195,959,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 262,966 duplication rate = 6.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9421 >>>>>>> ACTG content number of A's = 55,108,358 bp (28.12%) number of C's = 35,529,492 bp (18.13%) number of T's = 62,617,212 bp (31.95%) number of G's = 42,590,401 bp (21.73%) number of N's = 113,999 bp (0.06%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,852,270 number of insertions = 15,781 mapped reads with insertion percentage = 0.52% number of deletions = 70,404 mapped reads with deletion percentage = 2.3% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.6358X There is a 4.28% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% of reference with a coverageData >= 11X There is a 0% 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 11518116 0.0462109821583955 1.1818014382212365 chr2 243199373 14188903 0.058342679197614544 0.5866742149952232 chr3 198022430 1980687 0.01000233660398976 0.14841289787809467 chr4 191154276 19774246 0.10344652713915749 0.480577444487347 chr5 180915260 10851745 0.059982474667974385 0.3398251447681056 chr6 171115067 7747593 0.04527709415559531 0.30974547422282883 chr7 159138663 8953337 0.05626123049682779 0.41174860803945007 chr8 146364022 5320402 0.03635047689520311 1.215054328128693 chr9 141213431 5153285 0.03649288147385924 0.47084849042155424 chr10 135534747 8807454 0.06498299657430283 0.7046915120405534 chr11 135006516 8110469 0.06007464854511171 0.4369912952244096 chr12 133851895 21416945 0.16000479485180244 0.5520575829207734 chr13 115169878 11661207 0.10125223020554038 0.433529334280692 chr14 107349540 5211658 0.04854848935542714 0.3505715333891995 chr15 102531392 6577070 0.06414689073956979 0.3587634662285854 chr16 90354753 3815965 0.04223314074025525 0.3870279484418737 chr17 81195210 9234259 0.11372911037486079 0.5012400361698125 chr18 78077248 5430721 0.06955574305077966 1.255424268561087 chr19 59128983 3068771 0.05189960733807987 0.9142678013205648 chr20 63025520 6155089 0.09766026523858906 0.4955310106361909 chr21 48129895 4157416 0.08637907894874901 0.43558267191599515 chr22 51304566 1291111 0.025165615863508132 0.21220446739142168 chrMT 16571 62219 3.7546919316878884 3.4922721260914606 chrX 155270560 14889501 0.09589390931545555 0.47292684010963654 chrY 59373566 701917 0.011822045521065722 0.30218624617238815