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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,477,887 A→G 21.4% intergenic (+42/‑141) pstA → / → pstB phosphate transporter subunit/phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,477,8870AG21.4% 51.4 / 9.0 28intergenic (+42/‑141)pstA/pstBphosphate transporter subunit/phosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (14/8);  new base G (3/3);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 6.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTTGCGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGC  >  minE/2477820‑2477955
                                                                   |                                                                    
agcgtcgcatctggcataaacaaagcgcactttgctggtctgTTCCCCTCACCCTAACCATCTCCCCggag                                                                   <  1:2856639‑M2/29‑1 (MQ=255)
    tGCGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAggg                                                                 >  1:2999350/1‑69 (MQ=255)
      cGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCg                                                              <  1:200668/70‑1 (MQ=255)
       gaagaaTAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCATCTCCCCAGAgg                                                                  <  1:2244658/65‑1 (MQ=255)
         agaaTAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAggg                                                          <  1:1912480/71‑1 (MQ=255)
             gcataaacaaagcgcactttgctggtctgTTCCCCTCACCCTAACCCTCTCCCCGGAGGGGCg                                                              <  1:809041‑M2/34‑1 (MQ=255)
             gcataaacaaagcgcactttgctggtctgTTCCCCTCACCCTAACCCTCTCCCCGGAGGGGCGAGGGga                                                        <  1:3771594‑M2/40‑1 (MQ=255)
                taaacaaagcgcactttgctggtctgTTCCCCTCACCCTAACCCTCTCCCCGGAGGGGCGa                                                             >  1:3350532‑M2/27‑61 (MQ=255)
                 aaacaaagcgcactttgctggtctgTTCCCCTCACCCTAACCCTCTCCCCGGAGGGGCGCggg                                                          >  1:1333525‑M2/26‑63 (MQ=255)
                 aaacaaagcgcactttgctggtctgTTCCCCTCACCCTAACCCTCTCCCCGGAGGGGCGAggggactgt                                                    >  1:3146473‑M2/26‑66 (MQ=255)
                    caaagcgcactttgctggtctgTTCCCCTCACCCTAACCCTCTCCCCGGAGGGGCGAGGggactgtccggg                                               <  1:3898565‑M2/49‑3 (MQ=255)
                     gTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCagag                                                                   >  1:1083685/1‑50 (MQ=255)
                       tGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGa                                                             >  1:3862328/1‑54 (MQ=255)
                                         tttCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGCCCGAGCGCCGTTTTGACTCTGTaca                           >  1:1447284/1‑70 (MQ=255)
                                            ccccTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACgg                        <  1:3950522/70‑1 (MQ=255)
                                                  aCCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAacac                 >  1:628040/1‑71 (MQ=255)
                                                   cccTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCttttt                                      <  1:3423192/49‑1 (MQ=255)
                                                    ccTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGActc                                 <  1:1735534/53‑1 (MQ=255)
                                                    ccTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACtt               >  1:1166628/1‑71 (MQ=255)
                                                      tAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTg             >  1:34755/1‑71 (MQ=255)
                                                      tAAACCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTg             >  1:1577865/1‑71 (MQ=255)
                                                       aaCCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTAAACGGTTAACACTTTGc            >  1:3945448/1‑71 (MQ=255)
                                                        aCCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAac                   >  1:1304699/1‑63 (MQ=255)
                                                          ccTCTCCCCAGAGGGGCGAGGGGCCCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTg             >  1:2318072/1‑67 (MQ=255)
                                                            tctcCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACgg                        >  1:1823239/1‑54 (MQ=255)
                                                              tcCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTGGCCGGAt       >  1:3777795/1‑69 (MQ=255)
                                                                cccAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATg      <  1:1147372/68‑1 (MQ=255)
                                                                 ccAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATgcggc  >  1:3003638/1‑71 (MQ=255)
                                                                 ccAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATgcggc  <  1:2706250/71‑1 (MQ=255)
                                                                  cAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTaa                    >  1:488727/1‑52 (MQ=255)
                                                                   |                                                                    
TTTTTGCGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGC  >  minE/2477820‑2477955

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A