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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,472,806 C→T 15.0% D272D (GAC→GAT)  intS → predicted prophage CPS‑53 integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,472,8060CT15.0% 154.1 / 17.2 60D272D (GAC→GAT) intSpredicted prophage CPS‑53 integrase
Reads supporting (aligned to +/- strand):  ref base C (23/28);  new base T (7/2);  total (30/30)
Fisher's exact test for biased strand distribution p-value = 1.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.50e-01

TAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGTTTTTGCC  >  W3110S.gb/2472740‑2472872
                                                                  |                                                                  
tAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAgg                                                                >  1:4461466/1‑71 (MQ=255)
  ggATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGt                                                               <  1:1491777/70‑1 (MQ=255)
  ggATTATCACCATCGACGCCAGTGTGATGAAAGGACGAAAAATTCATGTGGTTCCTATGTCAGACCAgg                                                                <  1:3738611/69‑1 (MQ=255)
       aTCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGCTg                                                          <  1:1990420/70‑1 (MQ=255)
        tCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGaa                                                        <  1:1947832/71‑1 (MQ=255)
         cACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGAcc                                                                   <  1:3461552/59‑1 (MQ=255)
          aCCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAAc                                                       <  1:4435261/70‑1 (MQ=255)
           ccATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTg                                                          <  1:1652059/66‑1 (MQ=255)
           ccATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGa                                                         <  1:759284/67‑1 (MQ=255)
             aTCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTtct                                                   <  1:2723730/71‑1 (MQ=255)
                gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCAc                                                >  1:4399/1‑71 (MQ=255)
                gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCAc                                                >  1:3255460/1‑71 (MQ=255)
                gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAg                                                                 >  1:1611291/1‑54 (MQ=255)
                gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTtctc                                                  >  1:1425168/1‑69 (MQ=255)
                gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCAc                                                >  1:757143/1‑71 (MQ=255)
                gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCAc                                                >  1:762514/1‑71 (MQ=255)
                       gtgtGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTa                                         <  1:4455788/71‑1 (MQ=255)
                       gtgtGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTa                                         <  1:201013/71‑1 (MQ=255)
                        tgtgATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGAcc                                                                   <  1:310165/44‑1 (MQ=255)
                        tgtgATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGt                                                               <  1:3109437/48‑1 (MQ=255)
                         gtgATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTa                                                              >  1:2562006/1‑48 (MQ=255)
                         gtgATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTtc                                                    >  1:923151/1‑58 (MQ=255)
                          tgatgaAAGGACTCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCAc                                                <  1:2949505/61‑1 (MQ=255)
                          tgatgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAg                                                                 >  1:2223681/1‑44 (MQ=255)
                          tgatgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAg                                       >  1:2756044/1‑70 (MQ=255)
                            atgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAg                                                                 <  1:2545450/42‑1 (MQ=255)
                            atgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGt                                                               <  1:1164145/44‑1 (MQ=255)
                            atgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACTCTAAGCTc                                    <  1:4592700/71‑1 (MQ=255)
                            atgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTc                                    <  1:3845049/71‑1 (MQ=255)
                             tgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGCCCAg                                                                 >  1:4245475/1‑41 (MQ=255)
                              gaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCa                                                                  >  1:4400361/1‑39 (MQ=255)
                              gaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGt                                                               >  1:1993613/1‑42 (MQ=255)
                              gaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGt                                                               >  1:3646560/1‑42 (MQ=255)
                              gaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGt                                                            >  1:1066459/1‑45 (MQ=255)
                                 aGGACGCAAAATTCATGTGGTTCCTATGTCAGCCCAGGTAGTTGAACTTCTCACTACGCTaa                                        >  1:869615/1‑62 (MQ=255)
                                 aGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCACTACGCTaa                                        >  1:2262084/1‑62 (MQ=255)
                                    aCGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCa                            <  1:3032986/71‑1 (MQ=255)
                                        aaaaTTCATGTGGTTCCTATGTCAGACCAGGTAGTTTAACTtc                                                    <  1:875977/43‑1 (MQ=255)
                                         aaaTTCATGTGGTTCCTATGTCAGACCAGGTAGTTg                                                          >  1:3790222/1‑36 (MQ=255)
                                         aaaTTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACt                                                      <  1:1573015/40‑1 (MQ=255)
                                         aaaTTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACt                                                      >  1:738629/1‑40 (MQ=255)
                                             tCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTc                                    >  1:2775430/1‑54 (MQ=255)
                                             tCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGtct                   >  1:299725/1‑71 (MQ=255)
                                             tCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGtct                   >  1:144967/1‑71 (MQ=255)
                                              cATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGtct                   >  1:2080991/1‑70 (MQ=255)
                                              cATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGtct                   >  1:370934/1‑70 (MQ=255)
                                                 gtgGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGc                                      <  1:4271275/48‑1 (MQ=255)
                                                 gtgGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCa                 >  1:1481161/1‑69 (MQ=255)
                                                   ggTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTcc                                   <  1:4025853/49‑1 (MQ=255)
                                                       ccTATGTCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCag                >  1:3260258/1‑64 (MQ=255)
                                                       ccTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCaga               >  1:878424/1‑65 (MQ=255)
                                                       ccTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAgtttgt         >  1:3344145/1‑71 (MQ=255)
                                                         tATGTCAGACCAGTTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAgtttgtt        <  1:1771283/70‑1 (MQ=255)
                                                          aTGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCa                 <  1:4408999/60‑1 (MQ=255)
                                                           tGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCagag              <  1:2464355/62‑1 (MQ=255)
                                                           tGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGtttt      <  1:3844702/70‑1 (MQ=255)
                                                            gTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGc                                      <  1:3127955/37‑1 (MQ=255)
                                                            gTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCa                 <  1:2503471/58‑1 (MQ=255)
                                                             tCAGATCAGGTAGTTGAACTTCTCACTACGCTAAg                                       <  1:4368217/35‑1 (MQ=255)
                                                             tCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGc                                      <  1:2550403/36‑1 (MQ=255)
                                                              cAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGTTTTTGcc  >  1:2220230/1‑71 (MQ=255)
                                                                 aCCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCagag              <  1:459268/56‑1 (MQ=255)
                                                                  |                                                                  
TAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGTTTTTGCC  >  W3110S.gb/2472740‑2472872

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