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 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,113,649	C→T	50.8%	A1374T (GCA→ACA)	yghJ ←	predicted inner membrane lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,113,649	0	C	T	50.8%	‑6.0 / 92.4	61	A1374T (GCA→ACA)	yghJ	predicted inner membrane lipoprotein
Reads supporting (aligned to +/- strand): ref base C (11/19); new base T (18/13); total (29/32)
Fisher's exact test for biased strand distribution p-value = 1.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGATA  >  W3110S.gb/3113583‑3113715

gaggagTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTAc                                                                <  1:1338604/71‑1 (MQ=255)

     gTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATcag                                                           <  1:1441227/71‑1 (MQ=255)

           tCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATca                                                            <  1:3920150/64‑1 (MQ=255)

            cTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGa                                                       >  1:1018961/1‑68 (MQ=255)

                 tACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCAcc                                               >  1:4658901/1‑71 (MQ=255)

                    cATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTa                                                                 >  1:2316112/1‑50 (MQ=255)

                    cATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGTTCAccc                                              <  1:2594470/69‑1 (MQ=255)

                    cATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCAccc                                              <  1:1066318/69‑1 (MQ=255)

                     aTTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACa                                                               <  1:4076032/51‑1 (MQ=255)

                     aTTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACa                                                               <  1:3841473/51‑1 (MQ=255)

                     aTTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATcagca                                                         <  1:1296964/57‑1 (MQ=255)

                     aTTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATcagca                                                         <  1:2274669/57‑1 (MQ=255)

                      tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGc                                                                    >  1:4197645/1‑45 (MQ=255)

                      tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCAc                                          >  1:3899568/1‑71 (MQ=255)

                      tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTa                                                                 >  1:954645/1‑48 (MQ=255)

                      tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGc                                            >  1:2374764/1‑69 (MQ=255)

                       ttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGt                                                   <  1:5136011/61‑1 (MQ=255)

                       ttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGt                                                   <  1:5116878/61‑1 (MQ=255)

                        tCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACgg                                                    >  1:625294/1‑59 (MQ=255)

                         cTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCAccgc                                       >  1:4713368/1‑71 (MQ=255)

                           tggtatCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGc                                            >  1:2201521/4‑64 (MQ=255)

                           tGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGc                                            >  1:4594576/1‑64 (MQ=255)

                           tGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAccgccg                                     >  1:634993/1‑71 (MQ=255)

                           tGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAccgccg                                     >  1:1434655/1‑71 (MQ=255)

                                 cAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTa                                                                 <  1:2249871/37‑1 (MQ=255)

                                 cAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTa                                                                 <  1:160993/37‑1 (MQ=255)

                                  aaaGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:4859070/70‑1 (MQ=255)

                                  aaaGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:4598847/70‑1 (MQ=255)

                                  aaaGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:2591422/70‑1 (MQ=255)

                                    aGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCAt                            <  1:4105385/71‑1 (MQ=255)

                                     gTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCa                             >  1:3241625/1‑69 (MQ=255)

                                       ttttCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGcc                         >  1:3078424/1‑71 (MQ=255)

                                       ttttCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGcc                         >  1:942156/1‑71 (MQ=255)

                                        tttCTCTGCCCATTCCTTCAGCTGTGTGTACATca                                                            >  1:3015568/1‑35 (MQ=255)

                                        tttCTCTGCCCATTCCTTCAGCTGTGTGTACATca                                                            >  1:2079422/1‑35 (MQ=255)

                                        tttCTCTGCCCATTCCTTCAGCTGTGTGTACATca                                                            >  1:1722754/1‑35 (MQ=255)

                                        tttCTCTGCCCATTCCTTCAGCTGTGTGTACATca                                                            >  1:1514523/1‑35 (MQ=255)

                                        tttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCcgcg                                   >  1:2765914/1‑60 (MQ=255)

                                                cccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgtt                 <  1:5063957/70‑1 (MQ=255)

                                                cccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGttgttg                <  1:2150726/71‑1 (MQ=255)

                                                cccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGttgttg                <  1:4116225/71‑1 (MQ=255)

                                                   aTTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGctc             <  1:3057070/71‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:3328724/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:4389951/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:4347972/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:1441969/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:3334768/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:2561326/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                               <  1:2603240/52‑1 (MQ=255)

                                                    ttCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGctct            <  1:1518965/71‑1 (MQ=255)

                                                     tCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCtctc           >  1:541699/1‑71 (MQ=255)

                                                     tCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCtctc           >  1:535484/1‑71 (MQ=255)

                                                      ccTTCGGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTctcc          >  1:1052426/1‑71 (MQ=255)

                                                      ccTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCtctc           >  1:2103939/1‑70 (MQ=255)

                                                        ttCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTctcatc        >  1:3980445/1‑71 (MQ=255)

                                                         tCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGttgttg                >  1:1731929/1‑62 (MQ=255)

                                                          cAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTctcctc        >  1:2796688/1‑69 (MQ=255)

                                                          cAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTctcctc        <  1:4817160/69‑1 (MQ=255)

                                                           aGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCtctc           >  1:871450/1‑65 (MQ=255)

                                                              tgtgCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGACTGGTTGTTGCTCTCCTCCAGata  >  1:3930706/1‑71 (MQ=255)

                                                                tgCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCAt                            <  1:3793499/43‑1 (MQ=255)

                                                                tgCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGc                          <  1:4411864/45‑1 (MQ=255)

GAGGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGATA  >  W3110S.gb/3113583‑3113715

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A