Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 285,896 G→A 9.3% V168M (GTG→ATG)  yagG → CP4‑6 prophage; putative sugar transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913285,8960GA 9.3% 153.0 / 5.6 53V168M (GTG→ATG) yagGCP4‑6 prophage; putative sugar transporter
Reads supporting (aligned to +/- strand):  ref base G (24/24);  new base A (3/2);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.07e-01

CATCACCGCCGACCCGAAAGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCTTTGAGGTGCAGCCGGG  >  NC_000913/285796‑286032
                                                                                                       |                                                                                                                                        
catcaCCGCCGACCCGAAAGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTggg                                                                                                        <  1:354337/135‑1 (MQ=255)
catcaCCGCCGACCCGAAAGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTggg                                                                                                        >  2:354337/1‑135 (MQ=255)
    aCCGCCGACCCGAAAGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCAtgt                                                                                       >  3:926430/1‑148 (MQ=255)
                aaaGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGCGCATCATCGGCaaa                                                                                                                         >  2:170249/1‑102 (MQ=255)
                aaaGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCaaa                                                                                                                         <  1:170249/102‑1 (MQ=255)
                         cACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑Gt                                                                                                                                         <  4:188702/77‑1 (MQ=255)
                         cACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑Gt                                                                                                                                         >  3:188702/1‑77 (MQ=255)
                                 gCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTg                                                                                                                                        >  1:1029415/1‑70 (MQ=255)
                                 gCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTg                                                                                                                                        <  2:1029415/70‑1 (MQ=255)
                                  cAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGtgctgc                                                         <  4:926430/148‑1 (MQ=255)
                                   aGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCaa                                                                                                                          >  1:124626/1‑82 (MQ=255)
                                   aGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCaa                                                                                                                          <  2:124626/82‑1 (MQ=255)
                                         ggCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTg                                                                                                          <  4:646381/92‑1 (MQ=255)
                                         ggCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTg                                                                                                          >  3:646381/1‑92 (MQ=255)
                                              ttcttcCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGc                                                                                                       <  3:344661/90‑1 (MQ=255)
                                              ttcttcCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGc                                                                                                       >  4:344661/1‑90 (MQ=255)
                                                      ggcggcggcGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGcatca                                                                                                                                 >  4:235788/1‑56 (MQ=255)
                                                      ggcggcggcGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGcatca                                                                                                                                 <  3:235788/56‑1 (MQ=255)
                                                            ggcggGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCAtgtg                                                                                      <  3:682003/93‑1 (MQ=255)
                                                            ggcggGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCAtgtg                                                                                      >  4:682003/1‑93 (MQ=255)
                                                                        cgctATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTg                                                                         <  2:332689/94‑1 (MQ=255)
                                                                        cgctATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTg                                                                         >  1:332689/1‑94 (MQ=255)
                                                                         gctATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCt                  >  3:575220/1‑148 (MQ=255)
                                                                         gctATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCt                  <  4:575220/148‑1 (MQ=255)
                                                                            accAGCGGCAGCGCGATGCCGCTG‑‑‑ATGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATgtgcg                                                                                    <  3:1025917/77‑1 (MQ=38)
                                                                            accAGCGGCAGCGCGATGCCGCTG‑‑‑ATGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATgtgcg                                                                                    >  4:1025917/3‑79 (MQ=37)
                                                                             ccAGCGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTc                                                 <  4:193549/112‑1 (MQ=255)
                                                                             ccAGCGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTc                                                 >  3:193549/2‑113 (MQ=255)
                                                                               aGCGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCgtggtg                                                             <  2:744373/99‑1 (MQ=255)
                                                                               aGCGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCgtggtg                                                             >  1:744373/1‑99 (MQ=255)
                                                                               aGCGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCTTTGAgg            >  3:171459/1‑148 (MQ=255)
                                                                                gCGGCAGCGCGATGCCGCTGATAGCGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCt                                                                          <  3:633498/88‑1 (MQ=25)
                                                                                gCGGCAGCGCGATGCCGCTGATAGCGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCt                                                                          >  4:633498/1‑88 (MQ=25)
                                                                                gCGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCTTTGAGGt           <  4:171459/148‑1 (MQ=255)
                                                                                 cGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCt                        <  4:154627/134‑1 (MQ=255)
                                                                                 cGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCt                        >  3:154627/1‑134 (MQ=255)
                                                                                 cGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCaa                                >  3:412329/1‑126 (MQ=255)
                                                                                 cGGCAGCGCGATGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCaa                                <  4:412329/126‑1 (MQ=255)
                                                                                    cATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCg                                                                                                <  4:273177/59‑1 (MQ=255)
                                                                                    cATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCg                                                                                                >  3:273177/1‑59 (MQ=255)
                                                                                     aTCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACAcc                   >  1:789384/1‑135 (MQ=255)
                                                                                     aTCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACCACCAAAGAGCGCTAcccc                   <  2:789384/135‑1 (MQ=255)
                                                                                       cgcgCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGGGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTg                                               <  4:76931/105‑1 (MQ=255)
                                                                                       cgcgCTGCCGCTG‑‑‑ATGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTg                                               >  3:76931/1‑105 (MQ=255)
                                                                                         cgcTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCTTTGAGGTGCAGCgggg  >  1:873290/1‑148 (MQ=255)
                                                                                               cGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCt                        >  4:1061076/1‑120 (MQ=255)
                                                                                               cGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCt                        <  3:1061076/120‑1 (MQ=255)
                                                                                                gCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGt                                                                                                           <  4:212865/36‑1 (MQ=255)
                                                                                                gCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGt                                                                                                           >  3:212865/1‑36 (MQ=255)
                                                                                                gCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTg                                               >  1:140500/1‑96 (MQ=255)
                                                                                                gCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTg                                               <  2:140500/96‑1 (MQ=255)
                                                                                                gCTG‑‑‑ATGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGctc                                                       >  1:641486/1‑88 (MQ=255)
                                                                                                gCTG‑‑‑ATGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGctc                                                       <  2:641486/88‑1 (MQ=255)
                                                                                                       |                                                                                                                                        
CATCACCGCCGACCCGAAAGAGCGTCACGCCCTGCAGTCCTGGCGCTTCTTCCTGGCGGCGGCGGGCTCGCTCGCTATCAGCGGCATCGCGCTGCCGCTG‑‑‑GTGAGCATCATCGGCAAAGGGGACGAGCAGGTGGGCTACTTCGGCGCCATGTGCGTGCTGGGGCTGAGCGGCGTGGTGCTGCTCTACGTCTGCTTCTTCACGACCAAAGAGCGCTACACCTTTGAGGTGCAGCCGGG  >  NC_000913/285796‑286032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A