BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,718,454 number of mapped reads = 3,637,138 (97.81%) number of supplementary alignments = 328,069 (8.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,820,009 number of mapped paired reads (second in pair) = 1,817,129 number of mapped paired reads (both in pair) = 3,586,306 number of mapped paired reads (singletons) = 50,832 number of mapped bases = 429,284,138 bp number of sequenced bases = 429,059,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,661,671 duplication rate = 62.92% >>>>>>> Insert size mean insert size = 623,846.4511 std insert size = 7,350,253.3597 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.8919 >>>>>>> ACTG content number of A's = 130,517,166 bp (30.42%) number of C's = 83,182,150 bp (19.39%) number of T's = 129,925,171 bp (30.28%) number of G's = 85,429,514 bp (19.91%) number of N's = 5,239 bp (0%) GC percentage = 39.3% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 4,104,604 number of insertions = 43,632 mapped reads with insertion percentage = 1.16% number of deletions = 88,721 mapped reads with deletion percentage = 2.38% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.1387X std coverageData = 2.0685X There is a 3.26% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 1.79% of reference with a coverageData >= 3X There is a 1.43% of reference with a coverageData >= 4X There is a 1.03% of reference with a coverageData >= 5X There is a 0.84% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 33189904 0.13315876151819095 1.4379971943822896 chr2 243199373 34755214 0.142908320738146 6.014792277718658 chr3 198022430 34016368 0.1717803786167052 1.1549672705705762 chr4 191154276 25009301 0.1308330711890536 1.1048461128766511 chr5 180915260 27974643 0.15462843211788768 1.0873745318221475 chr6 171115067 24273049 0.14185220171172888 1.1947518022368997 chr7 159138663 21959919 0.13799235576083732 1.2836965512491898 chr8 146364022 26294090 0.17964858877682385 1.4692439044472725 chr9 141213431 18362820 0.13003593121393672 1.179529089408004 chr10 135534747 17781344 0.13119398821027053 2.10167165515908 chr11 135006516 15822788 0.11720018017500726 0.9541815695030845 chr12 133851895 21216576 0.15850784929118858 1.1029045401808144 chr13 115169878 10608113 0.09210839834353216 0.8506340445494167 chr14 107349540 12976632 0.12088204569856564 0.9606579233736672 chr15 102531392 15211548 0.14835990912909872 1.0514246627249377 chr16 90354753 13659848 0.15118018196563496 1.3114571747029766 chr17 81195210 16804409 0.20696305853510324 1.3381524311018367 chr18 78077248 8479758 0.10860728595352132 1.5652387659835838 chr19 59128983 6410980 0.1084236473338295 1.1064522220515687 chr20 63025520 18564574 0.2945564590343721 1.604179460747813 chr21 48129895 5422970 0.11267363039125683 0.9586664585045257 chr22 51304566 3110166 0.06062162186500126 0.6353633261216072 chrMT 16571 961263 58.00875022629896 47.35092574967395 chrX 155270560 15686783 0.1010287011266012 0.8762977078941557 chrY 59373566 731078 0.012313190014559678 0.46350957668402715