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 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,461,423 G→A 22.2% intergenic (‑331/+350) yfcV ← / ← sixA predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,461,4230GA22.2% 207.0 / 54.9 99intergenic (‑331/+350)yfcV/sixApredicted fimbrial‑like adhesin protein/phosphohistidine phosphatase
Reads supporting (aligned to +/- strand):  ref base G (39/38);  new base A (13/9);  total (52/47)
Fisher's exact test for biased strand distribution p-value = 6.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.91e-01

ATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAACACTATAG  >  W3110S.gb/2461359‑2461482
                                                                |                                                           
atatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACata                                                       >  1:957644/1‑71 (MQ=255)
atatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACata                                                       >  1:3519706/1‑71 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:750372/71‑1 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:2825202/71‑1 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACata                                                       >  1:4047681/1‑70 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACata                                                       >  1:2998601/1‑70 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACata                                                       >  1:1777555/1‑70 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACa                                                         <  1:1021283/68‑1 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACatat                                                      <  1:3891808/71‑1 (MQ=255)
 tatatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACata                                                       >  1:3821320/1‑70 (MQ=255)
  atatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      >  1:1054774/1‑70 (MQ=255)
  atatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      >  1:827495/1‑70 (MQ=255)
   tatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATaa                                                    <  1:1654266/71‑1 (MQ=255)
   tatTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACata                                                       >  1:2827326/1‑68 (MQ=255)
       tAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACata                                                       >  1:1550427/1‑64 (MQ=255)
       tAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGc                                                 <  1:279145/70‑1 (MQ=255)
       tAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGc                                                 <  1:3377901/70‑1 (MQ=255)
       tAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGc                                                 >  1:2024855/1‑70 (MQ=255)
       tAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGc                                                 >  1:3029002/1‑70 (MQ=255)
         gAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                                              <  1:1702323/71‑1 (MQ=255)
         gAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                                              <  1:3477004/71‑1 (MQ=255)
         gAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                                              <  1:336827/71‑1 (MQ=255)
         gAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                                              <  1:57346/71‑1 (MQ=255)
            aaaaCAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTgg                                           <  1:2512000/71‑1 (MQ=255)
                  ggAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTaa                                     <  1:659513/71‑1 (MQ=255)
                  ggAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTaa                                     <  1:2992722/71‑1 (MQ=255)
                  ggAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTaa                                     <  1:293254/71‑1 (MQ=255)
                     aGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc                                  >  1:1400414/1‑71 (MQ=255)
                         tatCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCg                                                <  1:3221651/53‑1 (MQ=255)
                         tatCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCg                                                <  1:2506250/53‑1 (MQ=255)
                         tatCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCg                                                <  1:373559/53‑1 (MQ=255)
                         tatCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCg                                                <  1:620907/53‑1 (MQ=255)
                         tatCAACAATGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCtt                              >  1:1546868/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATg                                                             >  1:422971/1‑38 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:385184/45‑1 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:2462473/45‑1 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:2827000/45‑1 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:3195070/45‑1 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:375137/45‑1 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACAtata                                                     >  1:2484601/1‑46 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACAtata                                                     >  1:1757857/1‑46 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACAtata                                                     >  1:3214604/1‑46 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACAtata                                                     >  1:1856834/1‑46 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACAtata                                                     >  1:1306152/1‑46 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACAtata                                                     >  1:1906684/1‑46 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGa                                               >  1:2301358/1‑52 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTACCCCGCtttt                            >  1:1142140/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCtttt                            >  1:2385438/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCtttt                            >  1:115929/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCtttt                            >  1:1869104/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCtttt                            >  1:2360561/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCtttt                            >  1:619342/1‑71 (MQ=255)
                           tCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCttt                             <  1:1993512/70‑1 (MQ=255)
                             aacaaTGAATGCCAATAGCTTAAAAAACAAACAATGAACATATaa                                                    >  1:41417/1‑45 (MQ=255)
                             aacaaTGAATGCCAATAGCTTAAAAAACAAACAATGAACATATaa                                                    >  1:2618653/1‑45 (MQ=255)
                             aacaaTGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCa                                         >  1:611922/1‑56 (MQ=255)
                             aacaaTGAATGCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCa                                         >  1:513852/1‑56 (MQ=255)
                              acaaTGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTc                         <  1:3248537/71‑1 (MQ=255)
                                aatgaatgCCAATAGCTTAAAAAACAAACAATGAACatat                                                      <  1:1800553/40‑1 (MQ=255)
                                 atgaatgCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGa                       >  1:1338251/1‑70 (MQ=255)
                                  tgaatgCCAATAGCTTAAAAAACAAACAATGAACATATaa                                                    >  1:3002109/1‑40 (MQ=255)
                                  tgaatgCCAATAGCTTAAAAAACAAACAATGAACATATaa                                                    >  1:1093335/1‑40 (MQ=255)
                                  tgaatgCCAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGata                     >  1:2516213/1‑71 (MQ=255)
                                   gaatgCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGata                     >  1:3502504/1‑70 (MQ=255)
                                     atgCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatataa                  <  1:1791193/71‑1 (MQ=255)
                                      tgCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatataat                 <  1:2932389/71‑1 (MQ=255)
                                         cAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGa                       <  1:3376562/62‑1 (MQ=255)
                                         cAATAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGa                       <  1:3945612/62‑1 (MQ=255)
                                          aaTAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat                    <  1:1863302/64‑1 (MQ=255)
                                          aaTAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat                    <  1:2725873/64‑1 (MQ=255)
                                           aTAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:3386765/71‑1 (MQ=255)
                                           aTAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:1471144/71‑1 (MQ=255)
                                           aTAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:1310011/71‑1 (MQ=255)
                                           aTAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCa                                         >  1:780176/1‑42 (MQ=255)
                                           aTAGCTTAAAAAACAAACAATAAACATATAATGCGATTGGCa                                         >  1:920003/1‑42 (MQ=255)
                                            tAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            >  1:802953/1‑70 (MQ=255)
                                            tAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            >  1:1025563/1‑70 (MQ=255)
                                            tAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:3527258/70‑1 (MQ=255)
                                            tAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            >  1:1765402/1‑70 (MQ=255)
                                            tAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            >  1:204304/1‑70 (MQ=255)
                                             aGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATaaa          >  1:4017309/1‑71 (MQ=255)
                                             aGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATaaa          >  1:2330813/1‑71 (MQ=255)
                                              gCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTc                         >  1:3106865/1‑55 (MQ=255)
                                              gCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATaaa          >  1:646447/1‑70 (MQ=255)
                                              gCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAac         <  1:173263/71‑1 (MQ=255)
                                              gCTTAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAac         <  1:92607/71‑1 (MQ=255)
                                                 tAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAacac       >  1:1210922/1‑70 (MQ=255)
                                                 tAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAacac       >  1:4024414/1‑70 (MQ=255)
                                                 tAAAAAACAAACAATAAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAacac       >  1:1159677/1‑70 (MQ=255)
                                                  aaaaaaCAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAacac       <  1:1613706/69‑1 (MQ=255)
                                                  aaaaaaCAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAACACta     >  1:2178872/1‑71 (MQ=255)
                                                   aaaaaCAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAACACta     <  1:2435189/70‑1 (MQ=255)
                                                   aaaaaCAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAACACta     <  1:1123582/70‑1 (MQ=255)
                                                     aaacaaacAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAACACTATAg  >  1:3368535/1‑71 (MQ=255)
                                                            caaTGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatataatata              >  1:3450261/1‑52 (MQ=255)
                                                             aaTGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:1902387/53‑1 (MQ=255)
                                                             aaTGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:1658347/53‑1 (MQ=255)
                                                              aTGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAAtatata            <  1:4022185/52‑1 (MQ=255)
                                                               tGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGa                       <  1:477742/40‑1 (MQ=255)
                                                               tGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGa                       <  1:3584907/40‑1 (MQ=255)
                                                                |                                                           
ATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAACACTATAG  >  W3110S.gb/2461359‑2461482

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A