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 F178 I0 R1 39 50.1 1100758 94.0% 1034712 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,440,085 G→T 100% intergenic (‑45/‑891) cspA ← / → xpaC cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0850GT99.3% 144.5 / ‑6.6 54intergenic (‑45/‑891)cspA/xpaCcold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (24/28);  minor base A (0/2);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTC  >  CP000730/1439951‑1440208
                                                                                                                                      |                                                                                                                           
aaaaTGTACGAATACGACATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAACGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTGATTCAATTTGCTTATTCTCatat                                                                                                                        >  1:273117/1‑140 (MQ=255)
   aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCGTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTTCAAGACTATACTTCCGTCGACAGGCTTATTCTCGCATTAc                                                                                                                     <  1:404992/140‑1 (MQ=255)
    tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAGTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTTTAATATTACa                                                                                                                    >  2:156597/1‑140 (MQ=255)
     gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATACTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa                                                                                                                   >  2:296243/1‑140 (MQ=255)
        cGAATACGTCATTTTCTCCTTCAACTTCGGTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaa                                                                                                                >  1:119604/1‑140 (MQ=255)
               gTCATTTTCTTCTTCAACTTCGAAAAAGCCAAATCCTTTTTCAGCGTTAAACCATTTAACTGCACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTAAAAAAAAAAAAAAAATACATg                                                                                                         <  2:525602/140‑1 (MQ=255)
               gTCATTTTCTCCTTCACCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg                                                                                                         <  2:50295/140‑1 (MQ=255)
                    tttCTCCTTCAACTGCTATACAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt                                                                                                    <  2:398364/140‑1 (MQ=255)
                      tctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAATACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAttt                                                                                                  <  2:266297/140‑1 (MQ=255)
                         cctttcaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                               <  2:276839/134‑1 (MQ=255)
                         ccTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                               <  1:325761/140‑1 (MQ=255)
                          cTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAAAAAAAATACCTGCAAATTTCACt                                                                                              >  2:536728/1‑140 (MQ=255)
                            tCAACTTCGATAAAGCCGAATCCTTTTTCAGCTTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCa                                                                                            <  1:220958/140‑1 (MQ=255)
                              aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                                                          <  1:220682/140‑1 (MQ=255)
                               aCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat                                                                                         <  2:363710/140‑1 (MQ=255)
                                  tCGTTAAAGCCGAACTCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAACATACATGCAAATTTCACTCAAATAtt                                                                                      <  2:341428/140‑1 (MQ=255)
                                  tCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAATACATGCAAATTTCACTCAAATATTc                                                                                     >  2:37483/1‑140 (MQ=255)
                                     aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                   <  2:147285/140‑1 (MQ=255)
                                     aTAAAGCCGAATCCTTTTTCAGCGTTAAAACATTTAACAGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCAGTCAATATGCTTATTAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                   <  2:27940/140‑1 (MQ=255)
                                        aaGCCTAATCCTTTTTCACCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                <  2:131906/140‑1 (MQ=255)
                                             gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                           <  1:95113/140‑1 (MQ=255)
                                             gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCAAATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                           <  1:67310/140‑1 (MQ=255)
                                               aTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg                                                                         <  2:94602/140‑1 (MQ=255)
                                                 ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaa                                                                       >  2:366229/1‑140 (MQ=255)
                                                      ttCAGCGTTAAACCATTTAGCTGTACCTTGTTTCATAATCTGAAGCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAttc                                                                  >  1:302385/1‑140 (MQ=255)
                                                        cAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                <  1:275903/140‑1 (MQ=255)
                                                           cGTTAAACCATTTAACTGTACCGTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTGAAATAGTCTTTGCAATATGGAATAATCATCTg                                                             <  1:119488/140‑1 (MQ=255)
                                                             ttAATCCATTTCACTGTACCTTGTTTCATAATATGAAACCTCCAAGACTAAAATTCCTTCAATATGCTTATTCTCATATTAGAAACAATACACGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                                                           <  1:52888/140‑1 (MQ=255)
                                                             ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAATACTAAAATTCATTCATTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                                                           <  1:431772/140‑1 (MQ=255)
                                                                       tAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                                 <  1:342311/140‑1 (MQ=255)
                                                                         aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattc                                               >  1:330170/1‑139 (MQ=255)
                                                                            gTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTCATTAACTTGTATTATAg                                            >  2:221681/1‑140 (MQ=255)
                                                                               ccTTGTTTCATAATCTGAAACCTCCAAGAATAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc                                         <  1:442380/140‑1 (MQ=255)
                                                                               ccTTGTTTCATAATCTGAAACCTACAAGACTAAAATTCAATCAATATGCTTATTCTAATATTACAAAAAATACAAGCAAATTTCAATCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc                                         <  1:137414/140‑1 (MQ=255)
                                                                               ccTTGTTTCATAATCTGAAAACTCCAAGAATAAAATTCATTCAATCTACTTATTGTCATATTAAAAAAAATACATGCCAAGTATACTCAAATATTCTTTGAAATATGGAATAAACAGCTGCTAAACtgatataatcgtcc                                         >  2:46048/1‑127 (MQ=255)
                                                                                 ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCATATATTCTTTGTAATATGGAATAATCATCTGCTTACCTTGTATTATAGTTCAg                                       >  2:42921/1‑140 (MQ=255)
                                                                                 ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                       >  1:278328/1‑140 (MQ=255)
                                                                                   gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                     <  1:338151/140‑1 (MQ=255)
                                                                                    tttCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtta                                    >  1:133036/1‑140 (MQ=255)
                                                                                      tCATGATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                  <  2:389252/140‑1 (MQ=255)
                                                                                      tCATAATCTGAAACCTCCAAGACTAAAATTCATTCATTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                  <  2:31503/140‑1 (MQ=255)
                                                                                      tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                  <  1:303376/140‑1 (MQ=255)
                                                                                        aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTACTTAACTTGTATTATAGTGCAGTTATTAc                                >  1:490697/1‑140 (MQ=255)
                                                                                         tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCCTCTGCTTACCTTGTATTGTAGTGAATTTATTAca                               >  2:19048/1‑139 (MQ=255)
                                                                                          aaTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                              >  2:519009/1‑140 (MQ=255)
                                                                                              tGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                          >  1:314710/1‑140 (MQ=255)
                                                                                                aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                        <  2:504968/140‑1 (MQ=255)
                                                                                                  aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaa                      >  1:155339/1‑140 (MQ=255)
                                                                                                  aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGAAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATCACCAAATTAcaa                      >  2:18521/1‑140 (MQ=255)
                                                                                                   ccTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaat                     >  1:383313/1‑140 (MQ=255)
                                                                                                      ccAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACAAAATTGcaataca                  >  2:433616/1‑140 (MQ=255)
                                                                                                           aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATTCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataat             <  2:21320/140‑1 (MQ=255)
                                                                                                                      ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc  >  1:172212/1‑140 (MQ=255)
                                                                                                                      ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc  >  2:185548/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                           
AAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTC  >  CP000730/1439951‑1440208

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A