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
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,181,764 C→T 16.5% intergenic (‑39/+19) ymfA ← / ← potD DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,181,7640CT16.5% 54.4 / 3.8 24intergenic (‑39/+19)ymfA/potDDUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base C (10/10);  new base T (2/2);  total (12/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

ACAGAAATGAGGATCAGTACCAGACCGATACCGAGGAATATACGAAAGAAAACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTAT  >  NC_000913/1181655‑1181898
                                                                                                             |                                                                                                                                      
ccaGAAATGAGGATCAGTACCAGACCGATACCGAGGAATATACGAAAGAAAACTTTTCTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTGGTATTAccgcc                                                                                                                                 <  1:299446/116‑1 (MQ=255)
acaGAAATGAGGATCAGTACCAGACCGATACCGAGGAATATACGAAAGAAAACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTGGTATTAccgcc                                                                                                                                 >  2:299446/1‑117 (MQ=255)
                gTACCAGACCGATACCGAGGAATATACGAAAGAAAACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCt                                                                                                                         <  4:767823/109‑1 (MQ=255)
                gTACCAGACCGATACCGAGGAATATACGAAAGAAAACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCt                                                                                                                         >  3:767823/1‑109 (MQ=255)
                                            aaagaaaACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCtt                                                                                                 <  1:958482/105‑1 (MQ=255)
                                            aaagaaaACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCtt                                                                                                 >  2:958482/1‑105 (MQ=255)
                                                      ttACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGaa                                                                                                                      >  4:825331/1‑74 (MQ=255)
                                                      ttACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGaa                                                                                                                      <  3:825331/74‑1 (MQ=255)
                                                      ttACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGataa                                                                                          >  3:507062/1‑102 (MQ=255)
                                                      ttACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGataa                                                                                          <  4:507062/102‑1 (MQ=255)
                                                                gACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATATCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCAt                                                                                >  2:944849/1‑102 (MQ=255)
                                                                gACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATATCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCAt                                                                                <  1:944849/102‑1 (MQ=255)
                                                                                          taaAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCtt                                                                                                 <  3:136804/59‑1 (MQ=255)
                                                                                          taaAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCtt                                                                                                 >  4:136804/1‑59 (MQ=255)
                                                                                           aaaaaaCGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAAtgctgc                                                                       >  3:281623/1‑84 (MQ=255)
                                                                                           aaaaaaCGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAAtgctgc                                                                       <  4:281623/84‑1 (MQ=255)
                                                                                                        tAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTc                                                                                  >  2:727005/1‑60 (MQ=255)
                                                                                                        tAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTc                                                                                  <  1:727005/60‑1 (MQ=255)
                                                                                                        tAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAgtgt       <  1:897231/135‑1 (MQ=255)
                                                                                                        tAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCAGTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAgtgt       >  2:897231/1‑135 (MQ=255)
                                                                                                         aaTACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTAt  <  3:182638/139‑1 (MQ=255)
                                                                                                         aaTACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTAt  >  4:182638/1‑139 (MQ=255)
                                                                                                          aTACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTa                                 >  2:1061681/1‑107 (MQ=255)
                                                                                                          aTACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTa                                 <  1:1061681/107‑1 (MQ=255)
                                                                                                             |                                                                                                                                      
ACAGAAATGAGGATCAGTACCAGACCGATACCGAGGAATATACGAAAGAAAACTTTACTGTCCTGACTCATTAGCCACATCCTTGCTAACTAAAAAACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTAT  >  NC_000913/1181655‑1181898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A