BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524749.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,430,056 number of mapped reads = 1,299,613 (90.88%) number of supplementary alignments = 4,747 (0.33%) number of secondary alignments = 0 number of mapped bases = 74,088,786 bp number of sequenced bases = 74,064,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,176 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4589 >>>>>>> ACTG content number of A's = 18,371,063 bp (24.8%) number of C's = 13,550,336 bp (18.3%) number of T's = 24,222,817 bp (32.7%) number of G's = 17,911,613 bp (24.18%) number of N's = 8,956 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 380,014 number of insertions = 5,399 mapped reads with insertion percentage = 0.41% number of deletions = 14,803 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.43% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2244X There is a 2.14% of reference with a coverageData >= 1X There is a 0.18% 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 5905218 0.023691888815795568 0.2882195004710515 chr2 243199373 6262863 0.025751970174692843 0.3680303559453209 chr3 198022430 4915562 0.02482325865812272 0.17511367969260894 chr4 191154276 4769176 0.024949355566600037 0.1963974276803438 chr5 180915260 4404475 0.024345514026843287 0.17103638724568174 chr6 171115067 4186205 0.02446426883028366 0.18607960170126098 chr7 159138663 4076151 0.02561383213330126 0.2593057680837629 chr8 146364022 3703082 0.02530049358714671 0.21480771567195953 chr9 141213431 3149623 0.02230399033361069 0.19578211203519433 chr10 135534747 3617260 0.0266888018022419 0.2573358272458861 chr11 135006516 3328556 0.02465478036630469 0.20564361424726105 chr12 133851895 3314509 0.024762510833335607 0.1745776807496439 chr13 115169878 2284740 0.01983799965473611 0.15365582548444331 chr14 107349540 2232839 0.02079970719949056 0.16200124404502134 chr15 102531392 2124539 0.02072086371362246 0.16140626511231645 chr16 90354753 2244021 0.02483567189874339 0.18712266615100223 chr17 81195210 2090594 0.02574775039069423 0.18555582665283665 chr18 78077248 1928035 0.02469394156925203 0.2918800840617368 chr19 59128983 1662940 0.028123940504777498 0.25404656413939897 chr20 63025520 1588670 0.02520677338322635 0.18308687127808762 chr21 48129895 990871 0.020587433236660915 0.17466353460352463 chr22 51304566 935114 0.018226720795182245 0.14965224641355188 chrMT 16571 24241 1.4628567980206384 1.5409813890023745 chrX 155270560 4100131 0.02640636447759318 0.19081640911989683 chrY 59373566 249371 0.004200034069033348 0.11737656542242643