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
A1 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,702,790	C→T	73.4%	intergenic (‑71/+201)	rnc ← / ← lepB	RNase III/leader peptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,702,790	0	C	T	73.4%	103.2 / 45.6	64	intergenic (‑71/+201)	rnc/lepB	RNase III/leader peptidase
Reads supporting (aligned to +/- strand): ref base C (13/4); new base T (26/21); total (39/25)
Fisher's exact test for biased strand distribution p-value = 1.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

CAATAAATAAATGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGCAACCTGGA  >  W3110S.gb/2702727‑2702860

cAATAAATAAATGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTc                                                                  >  1:308761/1‑70 (MQ=255)

cAATAAATAAATGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCg                                                                 >  1:1229915/1‑71 (MQ=255)

cAATAAATAAATGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCg                                                                 >  1:2769865/1‑71 (MQ=255)

 aataaataAATGCGTCAACAATACAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGc                                                                >  1:2627947/1‑71 (MQ=255)

     aataaatGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTg                                                              >  1:3437439/1‑69 (MQ=255)

     aataaatGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTg                                                              >  1:143026/1‑69 (MQ=255)

       taaatGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGcagt                                                          >  1:2750332/1‑71 (MQ=255)

         aatGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGcagttt                                                        <  1:873219/71‑1 (MQ=255)

         aatGAGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGcagttt                                                        <  1:85109/71‑1 (MQ=255)

             cGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGcagtttcagt                                                    >  1:300582/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTag                                                >  1:3722927/1‑70 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:2486699/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:715555/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:2362318/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:2918678/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:3022075/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:190074/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:311778/1‑71 (MQ=255)

                 aacaaTTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTAc                                                >  1:1563959/1‑71 (MQ=255)

                      ttCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:850618/71‑1 (MQ=255)

                      ttCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:3505911/71‑1 (MQ=255)

                      ttCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:3546558/71‑1 (MQ=255)

                      ttCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:723696/71‑1 (MQ=255)

                       tCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           >  1:1234897/1‑70 (MQ=255)

                         aGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTTCAGTTTCAGTTTACCGGtata                                         <  1:149579/70‑1 (MQ=255)

                         aGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         <  1:2682840/70‑1 (MQ=255)

                         aGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         <  1:146274/70‑1 (MQ=255)

                         aGCACACGAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         <  1:372587/70‑1 (MQ=255)

                             cacGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:3335655/64‑1 (MQ=255)

                             cacGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:271564/64‑1 (MQ=255)

                                gAAACAGACCTGATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:1402629/61‑1 (MQ=255)

                                    cAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTAcc                                               >  1:595886/1‑53 (MQ=255)

                                    cAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:3218185/1‑59 (MQ=255)

                                    cAGACCTGATATACATGGTTCTGCTAACTGATTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:1999491/1‑59 (MQ=255)

                                           gATATGCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:922859/1‑52 (MQ=39)

                                           gATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:2175821/1‑52 (MQ=255)

                                           gATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:661428/1‑52 (MQ=255)

                                           gATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:407447/1‑52 (MQ=255)

                                           gATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:783974/1‑52 (MQ=255)

                                           gATATACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:2554811/50‑1 (MQ=255)

                                            atatACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:3179124/49‑1 (MQ=255)

                                            atatACATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:2429355/49‑1 (MQ=255)

                                              ataCATGGTTCTGGTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCgtg                   >  1:2469683/1‑71 (MQ=255)

                                              ataCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:987678/1‑49 (MQ=255)

                                              ataCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:1387626/1‑49 (MQ=255)

                                              ataCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         >  1:3398044/1‑49 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:1675302/46‑1 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:561597/46‑1 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGta                                           <  1:2807315/46‑1 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATggg                                     >  1:3248018/1‑52 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCgtgt                  >  1:2359840/1‑71 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCgtgt                  >  1:3292432/1‑71 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCgtgt                  >  1:1293207/1‑71 (MQ=255)

                                               taCATGGTTCTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCgtgt                  >  1:1331021/1‑71 (MQ=255)

                                               taCATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGtata                                         <  1:3224503/48‑1 (MQ=255)

                                                 cATGGTTCTGCTAACTGCTTCGCTGCAGTTGCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGc                >  1:2668164/1‑71 (MQ=255)

                                                   tGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGAcc                                 <  1:3104955/52‑1 (MQ=255)

                                                     gTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTg            >  1:1392869/1‑71 (MQ=255)

                                                     gTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTg            >  1:18155/1‑71 (MQ=255)

                                                     gTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTg            >  1:1305116/1‑71 (MQ=255)

                                                        cTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGc          <  1:229938/70‑1 (MQ=255)

                                                        cTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGc          <  1:3305769/70‑1 (MQ=255)

                                                        cTGCTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGc          <  1:3310315/70‑1 (MQ=255)

                                                           cTAATTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGCAAcc      <  1:2356971/71‑1 (MQ=255)

                                                               cTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGCAACCTGGa  <  1:375707/71‑1 (MQ=255)

CAATAAATAAATGCGTCAACAATTCAGCACACGAAACAGACCTGATATACATGGTTCTGCTAACTGCTTCGCTGCAGTTTCAGTTTACCGGTATATGGGGACCAACGCTGTTTCGTGTGCCGTGGCAACCTGGA  >  W3110S.gb/2702727‑2702860

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