BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004134.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 = 1,450,047 number of mapped reads = 1,314,350 (90.64%) number of supplementary alignments = 10,453 (0.72%) number of secondary alignments = 0 number of mapped bases = 88,624,951 bp number of sequenced bases = 88,583,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,035 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6869 >>>>>>> ACTG content number of A's = 25,010,066 bp (28.23%) number of C's = 16,159,127 bp (18.24%) number of T's = 28,360,904 bp (32.02%) number of G's = 19,046,842 bp (21.5%) number of N's = 6,483 bp (0.01%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 789,497 number of insertions = 7,001 mapped reads with insertion percentage = 0.53% number of deletions = 25,387 mapped reads with deletion percentage = 1.91% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2848X There is a 2.56% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 5796764 0.02325676853579434 0.5406581033224328 chr2 243199373 5591682 0.022992172763537513 0.28516304761058325 chr3 198022430 3542739 0.017890594514974895 0.14466306569484444 chr4 191154276 4655771 0.024356091307107353 0.18318723519148045 chr5 180915260 5410325 0.029905299309743137 0.18978578686704808 chr6 171115067 6030869 0.0352445234994999 0.21667745199117186 chr7 159138663 4283620 0.026917531662308862 0.2972202466595216 chr8 146364022 7472566 0.05105466423982254 0.41493260315805697 chr9 141213431 4071701 0.028833666678632006 0.27948818068593634 chr10 135534747 5266257 0.038855401412303515 0.2865384500604175 chr11 135006516 3610348 0.026742027769978156 0.23506214640547887 chr12 133851895 4480305 0.03347210736164774 0.2040259075456363 chr13 115169878 3174731 0.027565636563407665 0.1834366919336893 chr14 107349540 2623699 0.024440710225679587 0.18056541066559628 chr15 102531392 3361934 0.03278931393031317 0.19694577177779268 chr16 90354753 2474834 0.027390191637179286 0.20104983005228938 chr17 81195210 2024739 0.024936680378066636 0.1882166055043028 chr18 78077248 3182245 0.04075764811792547 0.4934605475453385 chr19 59128983 1086183 0.018369722340734324 0.34383674303877376 chr20 63025520 2006568 0.0318373890449456 0.1983169699852268 chr21 48129895 774741 0.016096877003367656 0.15874131218318926 chr22 51304566 600014 0.011695138401521612 0.11549393927397095 chrMT 16571 31612 1.907670025948947 1.8293252158362536 chrX 155270560 6832132 0.04400146428273331 0.24893576095575767 chrY 59373566 238572 0.00401815178155208 0.10082896831369367