BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237331.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 = 2,715,881 number of mapped reads = 2,379,947 (87.63%) number of supplementary alignments = 27,683 (1.02%) number of secondary alignments = 0 number of mapped bases = 147,326,905 bp number of sequenced bases = 147,232,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 755,832 duplication rate = 20.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4535 >>>>>>> ACTG content number of A's = 38,757,030 bp (26.32%) number of C's = 24,892,196 bp (16.91%) number of T's = 49,936,718 bp (33.92%) number of G's = 33,630,463 bp (22.84%) number of N's = 15,993 bp (0.01%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 942,337 number of insertions = 9,810 mapped reads with insertion percentage = 0.41% number of deletions = 54,646 mapped reads with deletion percentage = 2.26% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.7177X There is a 1.68% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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% 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 12739834 0.05111254667646344 0.9364731380932201 chr2 243199373 6636779 0.027289457691159424 0.7337160786580207 chr3 198022430 14176448 0.07159011229182471 0.5881540001678437 chr4 191154276 7276351 0.03806533210902381 0.4389008898932106 chr5 180915260 6427493 0.035527644268371836 0.4205912492621437 chr6 171115067 24089031 0.14077679670370583 0.9484569452935196 chr7 159138663 9740757 0.061209242407673115 0.6242757221259213 chr8 146364022 11174425 0.07634680194836406 1.5934930944040842 chr9 141213431 3331193 0.023589774544887306 0.35894660750068336 chr10 135534747 10736794 0.07921801779731068 0.9697024861632721 chr11 135006516 1710771 0.012671766153864752 0.2819363397127823 chr12 133851895 3728155 0.027852836898573607 0.40801939370007945 chr13 115169878 7257348 0.06301428920502981 0.5939907584801537 chr14 107349540 3656169 0.034058543706847744 0.4014065777256325 chr15 102531392 2777045 0.027084826859660696 0.37827214233849893 chr16 90354753 1136689 0.01258029004849363 0.2540201902636348 chr17 81195210 3301022 0.04065537856235608 0.4733571034136569 chr18 78077248 3192015 0.04088278060210319 1.3936327181405093 chr19 59128983 3690079 0.06240728003050551 0.752410307402652 chr20 63025520 1371404 0.02175950313460325 0.33348154939661706 chr21 48129895 1094827 0.02274733821879312 0.3473901818895684 chr22 51304566 668791 0.013035701344788687 0.23710132554757482 chrMT 16571 3754 0.2265403415605576 0.7039757112689533 chrX 155270560 6993417 0.04504019950723434 0.496223602893924 chrY 59373566 416314 0.007011773555928913 0.22654699986233875