BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	3,920,280	A→T	6.7%	D29E (GAT→GAA)	cspA ←	major cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	3,920,280	0	A	T	6.7%	377.8 / 13.9	134	D29E (GAT→GAA)	cspA	major cold shock protein
Reads supporting (aligned to +/- strand): ref base A (75/50); new base T (2/7); total (77/57)
Fisher's exact test for biased strand distribution p-value = 3.67e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 142 total aligned reads displayed.

GGACACTTTCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAG  >  AP009048/3920211‑3920350

agtccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtatgatcacaca                                                                        >  1:3492413‑M2/66‑70 (MQ=255)

  tccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCt                                                                     >  1:867682‑M2/64‑71 (MQ=255)

    cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCtt                                                                    >  1:5386193‑M2/62‑70 (MQ=255)

         caatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                     >  1:5354825‑M2/57‑63 (MQ=255)

          aatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                     <  1:6948630‑M2/8‑2 (MQ=255)

            tttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCAt                                                           >  1:7514798‑M2/54‑71 (MQ=255)

             ttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTaga                                                                <  1:3285365‑M2/13‑1 (MQ=255)

                aaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTc                                                       <  1:3419370‑M2/22‑1 (MQ=255)

                 aaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTc                                                       <  1:197692‑M2/22‑1 (MQ=255)

                   acaagaacctcgcttaggcctgtgtccatattacgtgtgtaggatcACACATCTTTAGAGCCATCGTCAgg                                                    <  1:654038‑M2/25‑1 (MQ=255)

                     aagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAg                                                  <  1:1097515‑M2/27‑1 (MQ=255)

                      agaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                        <  1:6150488‑M2/21‑1 (MQ=255)

                      agaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCa                                                      >  1:6646401‑M2/44‑66 (MQ=255)

                       gaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCt                                                                     >  1:4992393‑M2/43‑50 (MQ=255)

                       gaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGt                                                 >  1:5372155‑M2/43‑70 (MQ=255)

                       gaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTACAGCCATCGTCAGGAGt                                                 >  1:5235775‑M2/43‑70 (MQ=255)

                         acctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgat                                              >  1:232036‑M2/41‑71 (MQ=255)

                         acctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtga                                               <  1:801963‑M2/30‑1 (MQ=255)

                          cctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                     <  1:5215165‑M2/8‑2 (MQ=255)

                          cctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                     <  1:6398362‑M2/8‑2 (MQ=255)

                          cctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                     <  1:7182446‑M2/8‑2 (MQ=255)

                          cctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatg                                             <  1:2940571‑M2/32‑1 (MQ=255)

                          cctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgat                                              >  1:2292871‑M2/40‑70 (MQ=255)

                           ctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatga                                            <  1:7197792‑M2/33‑1 (MQ=255)

                           ctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatga                                            <  1:3443232‑M2/33‑1 (MQ=255)

                             cgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGc                                                              >  1:5318725‑M2/37‑51 (MQ=255)

                              gcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagc                                         >  1:1705317‑M2/36‑71 (MQ=255)

                              gcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagc                                         >  1:3097144‑M2/36‑71 (MQ=255)

                               cttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagcc                                        <  1:1422422‑M2/37‑1 (MQ=255)

                               cttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagcc                                        <  1:1232531‑M2/37‑1 (MQ=255)

                                ttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGt                                                 <  1:575004‑M2/28‑1 (MQ=255)

                                ttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagc                                         >  1:3449140‑M2/34‑69 (MQ=255)

                                  aggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccg                                       <  1:3031375‑M2/38‑1 (MQ=255)

                                       tgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatga                                            >  1:2898015‑M2/27‑59 (MQ=255)

                                       tgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatga                                            >  1:7787615‑M2/27‑59 (MQ=255)

                                       tgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGt                                                 <  1:6275551‑M2/28‑1 (MQ=255)

                                        gtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccgaa                                     >  1:2111790‑M2/26‑65 (MQ=255)

                                        gtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagc                                         >  1:2613111‑M2/26‑61 (MQ=255)

                                        gtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCttt                               >  1:3670588‑M2/26‑71 (MQ=255)

                                         tgtccatattacgtgggtaggatcACACATCTTTag                                                                 >  1:1126185‑M2/25‑36 (MQ=255)

                                         tgtccatattacgtgggtaggatcACACATCTTTag                                                                 >  1:6509913‑M2/25‑36 (MQ=255)

                                         tgtccatattacgtgggtaggatcACACATCTTTAGAGCGATCGTCAGGAGTGATGAAGCCGAAGCCTTTg                              <  1:7873243‑M2/47‑1 (MQ=255)

                                           tccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatg                                             <  1:4478825‑M2/32‑1 (MQ=255)

                                           tccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaag                                          <  1:703645‑M2/35‑1 (MQ=255)

                                           tccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGt                             >  1:6293047‑M2/23‑70 (MQ=255)

                                           tccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGt                             <  1:3861145‑M2/48‑1 (MQ=255)

                                           tccatattaagtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgat                                              >  1:7773991‑M2/23‑53 (MQ=255)

                                            ccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGt                                                 <  1:6821378‑M2/28‑1 (MQ=255)

                                             catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                   >  1:6594242‑M2/21‑46 (MQ=255)

                                             catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                   >  1:4080277‑M2/21‑46 (MQ=255)

                                             catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaa                                           >  1:7479153‑M2/21‑54 (MQ=255)

                                             catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCa                           >  1:2437226‑M2/21‑70 (MQ=255)

                                             catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAg                          >  1:923276‑M2/21‑71 (MQ=255)

                                              atattacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                        <  1:5014616‑M2/21‑1 (MQ=255)

                                              atattacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                        <  1:5023668‑M2/21‑1 (MQ=255)

                                              atattacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                        <  1:1925510‑M2/21‑1 (MQ=255)

                                              atattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccg                                       >  1:2620245‑M2/20‑57 (MQ=255)

                                              atattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGc                         <  1:2205786‑M2/52‑1 (MQ=255)

                                              atattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGc                         <  1:3840826‑M2/52‑1 (MQ=255)

                                               tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCa                           <  1:2485313‑M2/50‑1 (MQ=255)

                                               tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCa                           <  1:6542364‑M2/50‑1 (MQ=255)

                                               tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCg                        >  1:4353723‑M2/19‑71 (MQ=255)

                                               tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCg                        >  1:4949435‑M2/19‑71 (MQ=255)

                                               tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCg                        >  1:445363‑M2/19‑71 (MQ=255)

                                                attacgtgggtaggatcACACATCTTTAGAGCCATCGTc                                                       >  1:7487105‑M2/18‑39 (MQ=255)

                                                attacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgat                                              <  1:5438676‑M2/31‑1 (MQ=255)

                                                 ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCa                                                      >  1:6036691‑M2/17‑39 (MQ=255)

                                                 ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCa                                                      >  1:6816189‑M2/17‑39 (MQ=255)

                                                 ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtg                                                >  1:4119830‑M2/17‑45 (MQ=255)

                                                 ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGtt                      >  1:2133366‑M2/17‑71 (MQ=255)

                                                 ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGt                       >  1:7145918‑M2/17‑70 (MQ=255)

                                                   acgtgggtaggatcACACATCTTTAGAGCCATCGTCa                                                      >  1:7853960‑M2/15‑37 (MQ=255)

                                                   acgtgggtaggatcACACATCTTTAGAGCCATCGTCa                                                      >  1:1280231‑M2/15‑37 (MQ=255)

                                                   acgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTg                     <  1:3047179‑M2/56‑1 (MQ=255)

                                                   acgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTg                     <  1:692443‑M2/56‑1 (MQ=255)

                                                   acgtgggtaggatcACACATCTTTAGAGACATCGTCAGGAGTGATgaa                                           >  1:1440330‑M2/15‑48 (MQ=255)

                                                     gtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                   >  1:5418720‑M2/13‑38 (MQ=255)

                                                     gtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                   >  1:3566045‑M2/13‑38 (MQ=255)

                                                     gtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                   >  1:2360558‑M2/13‑38 (MQ=255)

                                                       gggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCt                                 >  1:4051982‑M2/11‑54 (MQ=255)

                                                          taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccg                                       <  1:2811810‑M2/38‑1 (MQ=255)

                                                          taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAttt             <  1:1984569‑M2/64‑1 (MQ=255)

                                                          taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAttt             >  1:2221892‑M2/8‑71 (MQ=255)

                                                          taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAttt             <  1:2876151‑M2/64‑1 (MQ=255)

                                                            ggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaag                                          >  1:946571‑M2/6‑40 (MQ=255)

                                                            ggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGt                       >  1:7586601‑M2/6‑59 (MQ=255)

                                                            ggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGt                       >  1:5210084‑M2/6‑59 (MQ=255)

                                                              atcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccgaagcc                                  <  1:5971359‑M2/43‑1 (MQ=255)

                                                              atcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTAc          >  1:6175121‑M2/4‑70 (MQ=255)

                                                               tcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGa        >  1:7591840‑M2/3‑71 (MQ=255)

                                                               tcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGa        >  1:6509637‑M2/3‑71 (MQ=255)

                                                                cACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAttt             <  1:4303256‑M2/64‑1 (MQ=255)

                                                                 ACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCtt                                <  1:5051813‑M2/45‑1 (MQ=255)

                                                                  cacaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAc     >  1:7076464/1‑71 (MQ=255)

                                                                  cacaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAc     <  1:2764661/71‑1 (MQ=255)

                                                                  cacaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAc     >  1:4416146/1‑71 (MQ=255)

                                                                   acaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGa        >  1:6702453/1‑67 (MQ=255)

                                                                    caTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAc     >  1:858486/1‑69 (MQ=255)

                                                                     aTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAg  >  1:2433708/1‑71 (MQ=255)

                                                                     aTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAg  >  1:3836701/1‑71 (MQ=255)

GGACACTTTCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAG  >  AP009048/3920211‑3920350

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: `‑`