BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525079.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 = 1,296,028 number of mapped reads = 1,076,513 (83.06%) number of supplementary alignments = 3,636 (0.28%) number of secondary alignments = 0 number of mapped bases = 62,832,471 bp number of sequenced bases = 62,811,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,413 duplication rate = 4.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.856 >>>>>>> ACTG content number of A's = 16,112,090 bp (25.65%) number of C's = 11,749,680 bp (18.71%) number of T's = 20,217,354 bp (32.19%) number of G's = 14,725,291 bp (23.44%) number of N's = 6,788 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 308,163 number of insertions = 4,458 mapped reads with insertion percentage = 0.41% number of deletions = 13,014 mapped reads with deletion percentage = 1.2% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.2124X There is a 1.81% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 5207240 0.0208915828538698 0.3724048154700917 chr2 243199373 5443618 0.022383355404456573 0.2622033390048365 chr3 198022430 4253174 0.02147824365148938 0.16046824073963803 chr4 191154276 4178216 0.02185782127102404 0.18750044082538994 chr5 180915260 3907804 0.021600190055830557 0.16086417915366596 chr6 171115067 3654864 0.02135910100774469 0.16861034092998284 chr7 159138663 3507584 0.022041054850385416 0.23502694518226483 chr8 146364022 3256594 0.022249962494198198 0.21759296044330198 chr9 141213431 2688415 0.019037955391084577 0.17980899970876116 chr10 135534747 3145430 0.023207554296021227 0.24560004696739873 chr11 135006516 2968245 0.021985938812020007 0.18258878575791931 chr12 133851895 2874432 0.021474720249571363 0.16463161164588838 chr13 115169878 1985527 0.017239985267675634 0.14356348860761584 chr14 107349540 1949994 0.018164903175178954 0.1502204491406501 chr15 102531392 1898248 0.018513822576406647 0.14910574337094232 chr16 90354753 1894453 0.02096683281287925 0.16918137932870142 chr17 81195210 1757563 0.021646141441102253 0.1663373248632046 chr18 78077248 1693949 0.02169580823340495 0.2722468253212824 chr19 59128983 1306181 0.02209036810255979 0.263776296919501 chr20 63025520 1381148 0.021914107174363654 0.16594138291294414 chr21 48129895 862233 0.017914707688433562 0.16926644955245443 chr22 51304566 787831 0.01535596266421979 0.13663196586976176 chrMT 16571 6445 0.38893247239152734 0.7311233989527202 chrX 155270560 1996172 0.01285608810839608 0.1376804708834978 chrY 59373566 227111 0.0038251197511027044 0.16062894345944087