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 F169 I1 R1 59 38.6 831760 90.8% 755238 148.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 2,078,573 (T)7→8 coding (246/681 nt) USA300HOU_1935 ← hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,078,5661.T93.1% 88.8 / 1.1 29coding (253/681 nt)USA300HOU_1935hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base T (13/14);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

TGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTG‑TTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGATTGCA  >  CP000730/2078431‑2078697
                                                                                                                                        |                                                                                                                                     
tGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTG‑ttttttttgaca                                                                                                                           <  1:29016/148‑6 (MQ=255)
          atatGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACt                                                                                                                <  2:291975/148‑1 (MQ=255)
          atatGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACt                                                                                                                <  2:401622/148‑1 (MQ=255)
           tatGGAGTGGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGAATATAAACTAATAACAAGCGTTCCAATTAATGTTATAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTc                                                                                                               <  2:78523/148‑1 (MQ=255)
            atGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAATCTCa                                                                                                              <  2:40861/148‑1 (MQ=255)
            atGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCa                                                                                                              <  2:23189/148‑1 (MQ=255)
             tGCAGTTGACAAATAGATTGACTTTGGTTCGATCCCATCTGCTTCATAAGCCTATCAACTAATAACAAGCGTTCCAATTAATGTTTAAACCATGCCAGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAGACTCat                                                                                                             <  2:208302/148‑1 (MQ=255)
                  ttGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATaaa                                                                                                        >  1:146595/1‑148 (MQ=255)
                  ttGAAAAATAGATTGAATATAGATCAATCACATATGCTTTATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAAGATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTACCCTAAtataca                                                                                                        >  2:288984/1‑146 (MQ=255)
                         aTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCACTTAATGTTAAACCAATGCATGTAATATAGTTGGCATTAAGCAATTG‑TTTTTTTTCGACACTGGTAAACTCATATAAAaataat                                                                                                  >  2:62366/1‑148 (MQ=255)
                         aTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAataata                                                                                                 >  2:325997/1‑148 (MQ=255)
                               tGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATc                                                                                           >  1:410732/1‑148 (MQ=255)
                               tGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATc                                                                                           <  2:111155/148‑1 (MQ=255)
                                gAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCa                                                                                          >  2:176835/1‑148 (MQ=255)
                                 aaTTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCAt                                                                                         >  2:121951/1‑148 (MQ=255)
                                              cacaTCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCt                                                                            <  2:196375/148‑1 (MQ=255)
                                              cacaTCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAACAATATGAATCATTACCACCTAATCt                                                                            >  2:100982/1‑148 (MQ=255)
                                                            aaGCATATAAACTAATAACAAGCGTTCCAATAAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTTTaa                                                              >  2:331934/1‑148 (MQ=255)
                                                                      aCTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGAcc                                                    >  1:98809/1‑148 (MQ=255)
                                                                         aataaAAAGCGTTCCAATTAATATTAAAACAAAGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGc                                                 <  2:128974/148‑1 (MQ=255)
                                                                               aaGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTaa                                           <  1:81689/148‑1 (MQ=255)
                                                                                  cGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAAt                                        <  1:287666/148‑1 (MQ=255)
                                                                                                        aTGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGa                  <  2:250944/148‑1 (MQ=255)
                                                                                                          gCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑TTTTTTTTTAAACTCATATAAAAATAATATGAATCATTACCATCTAATCTACGATTGAGTCTAAATAATTGACCAGCATCTAAAATCCAAATAATCAATATTGTTTGACt                >  2:117548/1‑148 (MQ=255)
                                                                                                              gTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTtata            >  1:21199/1‑148 (MQ=255)
                                                                                                                  tataGTTGGCATTAAGCAATTGTTTTTTTT‑‑TTTTTTTTTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg        >  2:274030/1‑148 (MQ=255)
                                                                                                                  tataGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg        <  1:325997/148‑1 (MQ=255)
                                                                                                                   ataGTTGGCATTAAGCAATTG‑TTTTTTTTCGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg        <  1:62366/148‑1 (MQ=255)
                                                                                                                        tGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGATTGCa  <  1:176835/148‑1 (MQ=255)
                                                                                                                        tGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCAAAATAATCAATATTGTTGGACTTATAAAAGATTGCa  >  1:261429/1‑148 (MQ=255)
                                                                                                                                        |                                                                                                                                     
TGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTG‑TTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGATTGCA  >  CP000730/2078431‑2078697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A