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
A5 F8 I0 R2	53	71.6	5374071	98.5%	5293459	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,824,533:1	+G	100%	pseudogene (666/687 nt)	rph →	ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,824,533	1	.	G	95.2%	203.9 / 2.2	62	pseudogene (666/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand): ref base . (1/2); new base G (28/31); total (29/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

AGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑G‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT  >  W3110S.gb/3824464‑3824597

aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g                                                                    <  1:3091346/71‑1 (MQ=255)

aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g                                                                    <  1:3998775/71‑1 (MQ=255)

aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g                                                                    <  1:1450519/71‑1 (MQ=255)

 gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g                                                                  <  1:1215560/71‑1 (MQ=255)

 gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g                                                                  <  1:2937648/71‑1 (MQ=255)

  tGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑g                                                                <  1:3200147/71‑1 (MQ=255)

     aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑ggga                                                             <  1:1625377/71‑3 (MQ=255)

     aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g                                                                  >  1:401086/1‑67 (MQ=255)

      ggggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑gggaa                                                            >  1:3472279/1‑68 (MQ=255)

       gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑gg                                                               <  1:388939/67‑1 (MQ=255)

        ggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑GTG‑Gg‑aatc                                                          <  1:2204984/71‑1 (MQ=255)

         gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcg                                                         <  1:4456662/71‑1 (MQ=255)

         gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcg                                                         <  1:2059803/71‑1 (MQ=255)

            ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g                                                                    <  1:2738779/59‑1 (MQ=255)

             gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcgaatc                                                     >  1:4274375/1‑71 (MQ=255)

              cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcgaatc                                                     >  1:3612343/1‑70 (MQ=255)

                 aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCAtt                                                 <  1:3388543/71‑1 (MQ=255)

                 aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCAtt                                                 >  1:2757799/1‑71 (MQ=255)

                  aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTg                                                <  1:2909006/71‑1 (MQ=255)

                  aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑ggga                                                             <  1:633878/58‑3 (MQ=255)

                  aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑ggga                                                             <  1:4119877/58‑3 (MQ=255)

                      gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc                                            >  1:1702098/1‑71 (MQ=255)

                       aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCg                                           <  1:1448893/71‑1 (MQ=255)

                        gCCGTTCACGCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCg                                           >  1:1712121/1‑70 (MQ=255)

                        gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑g                                                                >  1:726700/1‑49 (MQ=255)

                        gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑g                                                                >  1:1947211/1‑49 (MQ=255)

                             tCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg                                        >  1:2140511/1‑68 (MQ=255)

                              cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑Aatccaatcca                                                   >  1:1904658/1‑56 (MQ=255)

                              cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCa                                                   >  1:3302379/1‑56 (MQ=255)

                              cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg                                     <  1:856093/70‑1 (MQ=255)

                              cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg                                     <  1:5323230/70‑1 (MQ=255)

                              cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg                                     <  1:5293998/70‑1 (MQ=255)

                              cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGAGACGCAg                                     <  1:2262496/70‑1 (MQ=255)

                               aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg                                     <  1:5300224/69‑1 (MQ=255)

                               aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGaa                                   <  1:1001932/71‑1 (MQ=255)

                               aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGa                                    <  1:950119/70‑1 (MQ=255)

                                 ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAgg                                 <  1:4097046/71‑1 (MQ=255)

                                 ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAgg                                 >  1:2778095/1‑71 (MQ=255)

                                  cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGa                                          >  1:2043063/1‑61 (MQ=255)

                                   aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCa                                                   >  1:132913/1‑51 (MQ=255)

                                   aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg                                        <  1:85282/62‑1 (MQ=255)

                                   aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAggcg                               >  1:3040977/1‑71 (MQ=255)

                                   aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAggcg                               <  1:2774330/71‑1 (MQ=255)

                                   aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACACAGAAggcg                               >  1:3598421/1‑71 (MQ=255)

                                     gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg                                        <  1:2852550/60‑1 (MQ=255)

                                      aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGaa                                   >  1:1324126/1‑64 (MQ=255)

                                      aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCAACGCAGAAGgcggcg                            >  1:2717052/1‑71 (MQ=255)

                                        gagCTACTCACCTTGTTGGCGCTGGCCCGA‑G‑G‑GGAAATCGAATCCATTGTAGc                                            >  1:2390187/1‑53 (MQ=255)

                                           cTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTa                                              >  1:4981970/1‑48 (MQ=255)

                                           cTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGc                                       <  1:2534944/55‑1 (MQ=255)

                                             aCTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGaa                                   >  1:4265161/1‑57 (MQ=255)

                                              cTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaa                     <  1:4369559/70‑1 (MQ=255)

                                                 accTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAggc                                <  1:1532321/54‑1 (MQ=255)

                                                 accTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt                  >  1:3446913/3‑70 (MQ=255)

                                                 accTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt                  <  1:4733650/68‑1 (MQ=255)

                                                  ccTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc                                            <  1:3793334/42‑1 (MQ=37)

                                                  ccTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc                                            <  1:4544717/42‑1 (MQ=37)

                                                  ccTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc                                            <  1:4647054/42‑1 (MQ=37)

                                                   cTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc                                            <  1:3439919/42‑1 (MQ=37)

                                                   cTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt               >  1:1539683/1‑71 (MQ=255)

                                                     tgttgGCGCTGTCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg                                        <  1:713087/44‑1 (MQ=25)

                                                     tgttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg                                        <  1:5249932/44‑1 (MQ=38)

                                                     tgttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttt             >  1:1303322/1‑71 (MQ=255)

                                                     tgttgGCGCTGGACCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGAc                                         >  1:3093496/1‑43 (MQ=25)

                                                      gttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt              <  1:4712786/69‑1 (MQ=255)

                                                      gttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt               >  1:5183624/1‑68 (MQ=255)

                                                      gttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGAAGCGACGCAg                                     <  1:4577174/46‑1 (MQ=37)

                                                       ttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt           <  1:2921643/71‑1 (MQ=255)

                                                         ggCGCTGCCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttt             >  1:4531883/1‑67 (MQ=255)

                                                          gcgctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTaa         <  1:2552263/67‑1 (MQ=255)

                                                          gcgctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAg        <  1:2132282/68‑1 (MQ=255)

                                                            gctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCa                                      >  1:1975428/2‑39 (MQ=37)

                                                            gctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc      >  1:5119228/2‑71 (MQ=255)

                                                             ctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc      >  1:2395866/1‑70 (MQ=255)

                                                              tGGCCCGA‑G‑GTGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCg     <  1:5060291/70‑1 (MQ=255)

                                                               ggCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGa                                    >  1:3290394/1‑38 (MQ=38)

                                                                gCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGCCt  >  1:962756/1‑71 (MQ=255)

AGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑G‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT  >  W3110S.gb/3824464‑3824597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A