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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,516,927 A→G 25.9% N151S (AAT→AGT)  ydcV → predicted spermidine/putrescine transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,516,9270AG25.9% 89.5 / 36.5 54N151S (AAT→AGT) ydcVpredicted spermidine/putrescine transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (21/19);  new base G (5/9);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 3.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

TGGAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAATGGC  >  W3110S.gb/1516861‑1516997
                                                                  |                                                                      
tGGAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGt                                                                     >  1:3218368/1‑70 (MQ=255)
tGGAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGt                                                                     >  1:2245328/1‑70 (MQ=255)
  gAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTc                                                                    <  1:3698003/69‑1 (MQ=255)
  gAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTc                                                                    <  1:686296/69‑1 (MQ=255)
  gAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTc                                                                    <  1:580999/69‑1 (MQ=255)
  gAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTc                                                                    <  1:2977002/69‑1 (MQ=255)
  gAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTc                                                                    <  1:1625455/69‑1 (MQ=255)
  gAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTc                                                                    <  1:4981987/69‑1 (MQ=255)
           tttttCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTCATCGCCCGttt                                                         <  1:1763058/71‑1 (MQ=255)
            ttttCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTCATCGCCCGtttt                                                        >  1:2787328/1‑71 (MQ=255)
             tttCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCa                                                                   >  1:2041733/1‑59 (MQ=255)
                  ccATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTcgccgc                                                  <  1:762953/71‑1 (MQ=255)
                  ccATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTcgccgc                                                  <  1:1331751/71‑1 (MQ=255)
                  ccATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTcgccgc                                                  <  1:416039/71‑1 (MQ=255)
                     tCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCAcc                                               >  1:117850/1‑71 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTCATCGCCCGTTTTCGCCGCAcctc                                             >  1:3989798/1‑71 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTCATCGCCCGTTTTCGCCGCAcctc                                             >  1:2965650/1‑71 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTCATCGCCCGTTTTCGCCGCAcctc                                             >  1:2670826/1‑71 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAAt                                                                       >  1:4047391/1‑45 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAAt                                                                       >  1:4594911/1‑45 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCAcctc                                             >  1:3881728/1‑71 (MQ=255)
                       gTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCAcctc                                             >  1:2023361/1‑71 (MQ=255)
                               tcATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAGTGTCATCGCCCGTTTTCGCCGCAcctcct                                           <  1:1560831/65‑1 (MQ=255)
                                  tGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCa                                                                   <  1:3386386/38‑1 (MQ=255)
                                  tGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCa                                                                   <  1:373572/38‑1 (MQ=255)
                                  tGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCt                                    <  1:4681202/69‑1 (MQ=255)
                                  tGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCt                                    <  1:2227081/69‑1 (MQ=255)
                                   gCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGtttt                                                        >  1:1691950/1‑48 (MQ=255)
                                   gCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGtttt                                                        >  1:4439023/1‑48 (MQ=255)
                                   gCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGtttt                                                        >  1:1467856/1‑48 (MQ=255)
                                    cGACTTTTTGTGTAGTTGCGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGtt                                >  1:1005575/1‑71 (MQ=255)
                                       cTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGtttt                                                        >  1:2654484/1‑44 (MQ=255)
                                       cTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGtttt                                                        >  1:5125909/1‑44 (MQ=255)
                                         ttttGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGc                           >  1:556585/1‑71 (MQ=255)
                                             gtgtAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTc                        <  1:5123419/70‑1 (MQ=255)
                                             gtgtAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTc                        <  1:3270153/70‑1 (MQ=255)
                                             gtgtAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTc                        <  1:2288653/70‑1 (MQ=255)
                                                     gtggtgTTTAACAGTGTCATCGCCCGTTTTCGCCGCAcctcc                                            >  1:787397/1‑42 (MQ=255)
                                                     gtggtgTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCt               >  1:4271509/1‑71 (MQ=255)
                                                      tggtgTTTAACAGTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCt               <  1:1365560/70‑1 (MQ=255)
                                                        gtgtTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCa                       <  1:2341762/60‑1 (MQ=255)
                                                        gtgtTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATc                <  1:61111/67‑1 (MQ=255)
                                                         tgtTTAACAGTGTCATCGCCCGTTTTCGCCGCAcctcct                                           <  1:2488786/39‑1 (MQ=255)
                                                           tttAACAGTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTc                        <  1:615929/56‑1 (MQ=255)
                                                           tttAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGa                              >  1:488698/1‑50 (MQ=255)
                                                           tttAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGa                              >  1:5054329/1‑50 (MQ=255)
                                                             tAACAATGTCATCGCCCGTTTTCGCCGCAcctcct                                           >  1:157400/1‑35 (MQ=255)
                                                             tAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAgg                            >  1:4924959/1‑50 (MQ=255)
                                                             tAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGcc        >  1:2956991/1‑70 (MQ=255)
                                                              aaCAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTc                        <  1:4424689/53‑1 (MQ=255)
                                                              aaCAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCa       <  1:2853252/70‑1 (MQ=255)
                                                               aCAGTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAAt     <  1:3327118/71‑1 (MQ=255)
                                                               aCAGTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAAt     <  1:1608172/71‑1 (MQ=255)
                                                                cAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATgg                   <  1:4443534/56‑1 (MQ=255)
                                                                  aTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAAtggc  <  1:1466702/71‑1 (MQ=255)
                                                                  aTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAAtggc  <  1:4746444/71‑1 (MQ=255)
                                                                  aTGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAAt     >  1:1262795/1‑68 (MQ=255)
                                                                  |                                                                      
TGGAGCCGGGATTTTTCACCATCGTGGTCGGTCATGCGACTTTTTGTGTAGTTGTGGTGTTTAACAATGTCATCGCCCGTTTTCGCCGCACCTCCTGGAGTCTGGTTGAGGCGTCAATGGATCTTGGGGCCAATGGC  >  W3110S.gb/1516861‑1516997

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