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
A9 F1 I1 R1	64	69.7	3300380	93.4%	3082554	111.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,253,271	G→A	A292V (GCC→GTC)	nupX ←	nucleoside permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,253,271	0	G	A	92.6%	159.6 / 3.8	54	A292V (GCC→GTC)	nupX	nucleoside permease
Reads supporting (aligned to +/- strand): ref base G (1/3); new base A (28/22); total (29/25)
Fisher's exact test for biased strand distribution p-value = 3.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

TGAGATAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCAG  >  NC_000913/2253137‑2253403

tGAGATAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATg                                                                                                                                  >  2:1613209/1‑139 (MQ=255)

  agaTAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGtt                                                                                                                                <  1:1613209/139‑1 (MQ=255)

                         tGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATTACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                         <  2:493341/139‑1 (MQ=255)

                               tttCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGccgccg                                                                                                   >  1:487930/1‑139 (MQ=255)

                                   tGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                               <  1:131478/139‑1 (MQ=255)

                                          tCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAaaaccaaac                                                                                                                     <  1:1116317/110‑1 (MQ=255)

                                          tCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAaaaccaaac                                                                                                                     >  2:1116317/1‑110 (MQ=255)

                                               cTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                       <  2:1441830/119‑1 (MQ=255)

                                               cTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                       <  2:120302/119‑1 (MQ=255)

                                               cTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                       >  1:120302/1‑119 (MQ=255)

                                               cTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                       >  1:1441830/1‑119 (MQ=255)

                                                    ggCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCa                                                                              <  2:1515007/139‑1 (MQ=255)

                                                    ggCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                               <  2:1532061/122‑1 (MQ=255)

                                                    ggCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                               >  1:1532061/1‑122 (MQ=255)

                                                     gCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCaa                                                                             <  2:1154032/139‑1 (MQ=255)

                                                          aTTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAAACTAAAATGGGCTCAAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAAGGCAattatt                                                                        >  1:1124729/1‑139 (MQ=37)

                                                               cATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGcaac                                                                   <  2:635120/139‑1 (MQ=255)

                                                                 tCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGcaacaa                                                                 <  2:226584/139‑1 (MQ=255)

                                                                   aCTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAAt                                                               <  2:178341/139‑1 (MQ=255)

                                                                       cAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCg                                                                                          <  2:856057/108‑1 (MQ=255)

                                                                       cAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCg                                                                                          >  1:856057/1‑108 (MQ=255)

                                                                               acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                               <  1:637529/95‑1 (MQ=255)

                                                                               acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                               >  2:637529/1‑95 (MQ=255)

                                                                               acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAAt                                                                                     <  1:1086408/105‑1 (MQ=255)

                                                                               acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAAt                                                                                     >  2:1086408/1‑105 (MQ=255)

                                                                               acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACt                                                   >  1:1115587/1‑139 (MQ=255)

                                                                                    tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                       <  1:632554/82‑1 (MQ=255)

                                                                                    tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                       >  2:632554/1‑82 (MQ=255)

                                                                                    tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAaaccaaacca                                                                                                                   <  2:1025085/70‑1 (MQ=255)

                                                                                    tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAaaccaaacca                                                                                                                   >  1:1025085/1‑70 (MQ=255)

                                                                                         cACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCacac                                         >  1:1108324/1‑139 (MQ=255)

                                                                                           cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATcaccac                                                    <  2:694686/126‑1 (MQ=255)

                                                                                           cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATcaccac                                                    >  1:694686/1‑126 (MQ=255)

                                                                                           cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCt                                       >  1:475154/1‑139 (MQ=255)

                                                                                           cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCt                                       >  2:172217/1‑139 (MQ=255)

                                                                                            gCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTg                                      >  2:93657/1‑139 (MQ=255)

                                                                                               aGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTgcgg                                   >  2:1092694/1‑139 (MQ=255)

                                                                                                      ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                         >  1:113365/1‑62 (MQ=255)

                                                                                                      ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                         <  2:113365/62‑1 (MQ=255)

                                                                                                      ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAAc                                                                                 >  1:1193688/1‑86 (MQ=255)

                                                                                                      ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAAc                                                                                 <  2:1193688/86‑1 (MQ=255)

                                                                                                      ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGAtttt                            >  2:938895/1‑139 (MQ=255)

                                                                                                      ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGAtttt                            >  1:185907/1‑139 (MQ=255)

                                                                                                          cagGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGc                        >  1:732933/1‑139 (MQ=255)

                                                                                                           agGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGcc                       <  2:1108324/139‑1 (MQ=255)

                                                                                                               aaCCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGt                   >  1:126812/1‑139 (MQ=255)

                                                                                                                    aaaaTGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGACATTg              >  1:411702/1‑139 (MQ=255)

                                                                                                                           aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                         <  2:1494249/41‑1 (MQ=255)

                                                                                                                           aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                         >  1:1494249/1‑41 (MQ=255)

                                                                                                                           aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTg                                                                       <  2:1074075/75‑1 (MQ=255)

                                                                                                                           aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTg                                                                       >  1:1074075/1‑75 (MQ=255)

                                                                                                                           aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGt       >  2:119343/1‑139 (MQ=255)

                                                                                                                               cAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCa   <  1:119343/139‑1 (MQ=255)

                                                                                                                                aGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCAg  <  1:172217/139‑1 (MQ=255)

TGAGATAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCAG  >  NC_000913/2253137‑2253403

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A